Open Provenance Model

Names
More detailed information about this field from each metasource.

Open Provenance Model
metasource: Fairsharing.org
version: None

OPM
metasource: Fairsharing.org
version: None

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Orientations of Proteins in Membranes database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

opm
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

Other names: OPM, Orientations of Proteins in Membranes database, opm

The Open Provenance Model (OPM) is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.

Webpage:

https://doi.org/10.1016/j.future.2010.07.005

Publications:

Publications
More detailed information about this field from each metasource.

OPM database and PPM web server: resources for positioning of proteins in membranes
PMID: 21890895
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

https://doi.org/10.1016/j.future.2010.07.005
metasource: Fairsharing.org
version: None

http://dx.doi.org/10.1093/nar/GKR703
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

OPM database and PPM web server: resources for positioning of proteins in membranes PubMed citations: 533.

533 articles citing: OPM database and PPM web server: resources for positioning of proteins in membranes

Reverse Genomics: Design of Universal Epitope Sets to Isolate All Saccharibacteria Members from the Human Oral Cavity. PMID:35336177
SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. PMID:35328409
Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine. PMID:35309507
Inhibition of N-type calcium ion channels by tricyclic antidepressants - experimental and theoretical justification for their use for neuropathic pain. PMID:35308021
Modeling of mutant superoxide dismutase 1 octamers with cross-linked disulfide bonds. PMID:35279789
Mechanistic insight into the impact of a bivalent ligand on the structure and dynamics of a GPCR oligomer. PMID:35242285
Proteome based mapping and molecular docking revealed DnaA as a potential drug target against Shigella sonnei. PMID:35241965
The oxytocin signaling complex reveals a molecular switch for cation dependence. PMID:35241813
Repurposing Based Identification of Novel Inhibitors against MmpS5-MmpL5 Efflux Pump of Mycobacterium smegmatis: A Combined In Silico and In Vitro Study. PMID:35203542
High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport. PMID:35181664
Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage. PMID:35180220
Structure and receptor recognition by the Lassa virus spike complex. PMID:35173332
A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States. PMID:35163095
Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning. PMID:35152294
Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor. PMID:35140883
Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential. PMID:35139120
SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency. PMID:35130329
Bridged Piperidine Analogues of a High Affinity Naphthalene-Based P2Y14R Antagonist. PMID:35113556
Effects of the N-terminal dynamics on the conformational states of human dopamine transporter. PMID:35101818
Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. PMID:35080979
Connexons Coupling to Gap Junction Channel: Potential Role for Extracellular Protein Stabilization Centers. PMID:35053197
Anionic Lipids Confine Cytochrome c2 to the Surface of Bioenergetic Membranes without Compromising Its Interaction with Redox Partners. PMID:35025510
Current status of PTMs structural databases: applications, limitations and prospects. PMID:35020020
The Structural Basis of Peptide Binding at Class A G Protein-Coupled Receptors. PMID:35011444
Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain. PMID:35008764
Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. PMID:34969836
Structure and ion-release mechanism of PIB-4-type ATPases. PMID:34951590
Modelling of the Citrus CCD4 Family Members: In Silico Analysis of Membrane Binding and Substrate Preference. PMID:34948418
Dynamic Coupling of Tyrosine 185 with the Bacteriorhodopsin Photocycle, as Revealed by Chemical Shifts, Assisted AF-QM/MM Calculations and Molecular Dynamic Simulations. PMID:34948384
A Conserved Allosteric Site on Drug-Metabolizing CYPs: A Systematic Computational Assessment. PMID:34948012
Single-Walled Carbon Nanotubes Inhibit TRPC4-Mediated Muscarinic Cation Current in Mouse Ileal Myocytes. PMID:34947764
Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. PMID:34932329
Molecular Investigation of Chicken Acid-Sensing Ion Channel 1 β11-12 Linker Isomerization and Channel Kinetics. PMID:34924957
Development of Human Recombinant Leptospirosis Vaccines. PMID:34914055
A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. PMID:34911545
Assembly and Analysis of Cell-Scale Membrane Envelopes. PMID:34910495
The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface. PMID:34901881
TonB-dependent receptor epitopes expressed in M. bovis BCG induced significant protection in the hamster model of leptospirosis. PMID:34893930
State-Targeting Stabilization of Adenosine A2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein. PMID:34884716
Structural Modelling of KCNQ1 and KCNH2 Double Mutant Proteins, Identified in Two Severe Long QT Syndrome Cases, Reveals New Insights into Cardiac Channelopathies. PMID:34884666
Structures of the σ2 receptor enable docking for bioactive ligand discovery. PMID:34880501
A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum Ca2+-ATPase. PMID:34875216
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. PMID:34874077
RCSB Protein Data Bank: Improved Annotation, Search, and Visualization of Membrane Protein Structures Archived in the PDB. PMID:34864908
B0AT1 Amino Acid Transporter Complexed With SARS-CoV-2 Receptor ACE2 Forms a Heterodimer Functional Unit: In Situ Conformation Using Radiation Inactivation Analysis. PMID:34847569
A3 adenosine receptor agonists containing dopamine moieties for enhanced interspecies affinity. PMID:34844790
Presynaptic Release-Regulating Alpha2 Autoreceptors: Potential Molecular Target for Ellagic Acid Nutraceutical Properties. PMID:34829630
Ceramide-1-phosphate transfer protein promotes sphingolipid reorientation needed for binding during membrane interaction. PMID:34808193
Understanding the role of the CB1 toggle switch in interaction networks using molecular dynamics simulation. PMID:34785728
Building Structural Models of a Whole Mycoplasma Cell. PMID:34774566
DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence. PMID:34765094
GPCR activation mechanisms across classes and macro/microscales. PMID:34759375
Structure of the hexameric fungal plasma membrane proton pump in its autoinhibited state. PMID:34757782
Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. PMID:34733103
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0. PMID:34716622
The conformational cycle of prestin underlies outer-hair cell electromotility. PMID:34695838
Modeling the Heterodimer Interfaces of Melatonin Receptors. PMID:34690701
Functional molecular switches of mammalian G protein-coupled bitter-taste receptors. PMID:34687318
Structural and functional stability of the sulfur-free surfactant protein B peptide mimic B-YL in synthetic surfactant lipids. PMID:34686153
Hydroxylated Fatty Acids: The Role of the Sphingomyelin Synthase and the Origin of Selectivity. PMID:34677553
Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. PMID:34671734
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PMID:34648493
Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways. PMID:34638633
Spatial bias in cAMP generation determines biological responses to PTH type 1 receptor activation. PMID:34609896
Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations. PMID:34589184
Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme-substrate recognition. PMID:34584735
Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H+ symporter STP10. PMID:34556835
Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain. PMID:34548399
Scaffold Hybridization Strategy Leads to the Discovery of Dopamine D3 Receptor-Selective or Multitarget Bitopic Ligands Potentially Useful for Central Nervous System Disorders. PMID:34529404
Structural insights into hepatitis C virus receptor binding and entry. PMID:34526719
Principal component analysis of alpha-helix deformations in transmembrane proteins. PMID:34525125
Ultrafast energy transfer between lipid-linked chromophores and plant light-harvesting complex II. PMID:34524278
Open-state structure and pore gating mechanism of the cardiac sodium channel. PMID:34520724
Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae. PMID:34518546
Lactococcus lactis Resistance to Aureocin A53- and Enterocin L50-Like Bacteriocins and Membrane-Targeting Peptide Antibiotics Relies on the YsaCB-KinG-LlrG Four-Component System. PMID:34516250
Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. PMID:34504004
Untangling the web of 5-lipoxygenase-derived products from a molecular and structural perspective: The battle between pro- and anti-inflammatory lipid mediators. PMID:34487716
In silico identification and experimental validation of cellular uptake and intracellular labeling by a new cell penetrating peptide derived from CDN1. PMID:34463179
Potent Activity of Hybrid Arthropod Antimicrobial Peptides Linked by Glycine Spacers. PMID:34445625
TRPM8 Channels: Advances in Structural Studies and Pharmacological Modulation. PMID:34445208
Effective Use of Empirical Data for Virtual Screening against APJR GPCR Receptor. PMID:34443478
Nicastrin-Like, a Novel Transmembrane Protein from Trypanosoma cruzi Associated to the Flagellar Pocket. PMID:34442829
Identification of a specific surface epitope of OmpC for Escherichia coli O157:H7 with protein topology facilitated affinity mass spectrometry. PMID:34432131
The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter. PMID:34417466
Structural insights into a novel family of integral membrane siderophore reductases. PMID:34417315
Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. PMID:34417297
Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins. PMID:34417182
The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites. PMID:34408000
The evolutionary history of topological variations in the CPA/AT transporters. PMID:34403419
Cryo-EM structures of the TTYH family reveal a novel architecture for lipid interactions. PMID:34385445
Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations. PMID:34377364
Comparative Molecular Dynamics Investigation of the Electromotile Hearing Protein Prestin. PMID:34361083
Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. PMID:34354057
In silico identification and experimental validation of cellular uptake by a new cell penetrating peptide P1 derived from MARCKS. PMID:34338123
Membrane-Facilitated Receptor Access and Binding Mechanisms of Long-Acting β2-Adrenergic Receptor Agonists. PMID:34334369
In Silico Prediction of Permeability Coefficients. PMID:34302680
Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation. PMID:34302674
Memdock: An α-Helical Membrane Protein Docking Algorithm. PMID:34302673
Membrane Protein Engineering with Rosetta. PMID:34302669
Strained contacts with the cell membrane may influence ligand affinity to G protein coupled receptors: a case of free fatty acid receptor 1 agonists. PMID:34294008
Structural Modeling and in planta Complementation Studies Link Mutated Residues of the Medicago truncatula Nitrate Transporter NPF1.7 to Functionality in Root Nodules. PMID:34276736
An Independent Evolutionary Origin for Insect Deterrent Cucurbitacins in Iberis amara. PMID:34264303
Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis. PMID:34240914
A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins. PMID:34236204
A two-stage computational approach to predict novel ligands for a chemosensory receptor. PMID:34235481
Double Arylation of the Indole Side Chain of Tri- and Tetrapodal Tryptophan Derivatives Renders Highly Potent HIV-1 and EV-A71 Entry Inhibitors†. PMID:34229438
Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin. PMID:34226545
N-(Anilinoethyl)amide Melatonergic Ligands with Improved Water Solubility and Metabolic Stability. PMID:34213063
The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins. PMID:34206634
Structure-based insights into evolution of rhodopsins. PMID:34193947
Determination of the membrane topology of PORCN, an O-acyl transferase that modifies Wnt signalling proteins. PMID:34186010
Unexpected Gating Behaviour of an Engineered Potassium Channel Kir. PMID:34179097
Recent advances in the structural diversity of reaction centers. PMID:34173168
Residue 6.43 defines receptor function in class F GPCRs. PMID:34168128
Identification of binding sites for ivacaftor on the cystic fibrosis transmembrane conductance regulator. PMID:34142049
Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution. PMID:34134992
Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT. PMID:34112694
Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides. PMID:34105971
The push-to-open mechanism of the tethered mechanosensitive ion channel NompC. PMID:34101577
Inward-facing glycine residues create sharp turns in β-barrel membrane proteins. PMID:34097860
Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR. PMID:34091964
Mutation of a conserved glutamine residue does not abolish desensitization of acid-sensing ion channel 1. PMID:34061161
GPCRsignal: webserver for analysis of the interface between G-protein-coupled receptors and their effector proteins by dynamics and mutations. PMID:34060630
Molecular model of a sensor of two-component signaling system. PMID:34031444
Structural insights on ligand recognition at the human leukotriene B4 receptor 1. PMID:34016973
Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia). PMID:34016058
CD9 inhibition reveals a functional connection of extracellular vesicle secretion with mitophagy in melanoma cells. PMID:34012515
Molecular mechanisms of ion conduction and ion selectivity in TMEM16 lipid scramblases. PMID:33990555
Revealing the activation mechanism of autoinhibited RalF by integrated simulation and experimental approaches. PMID:33980916
Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans. PMID:33969560
Architecture of the membrane-bound cytochrome c heme lyase CcmF. PMID:33958791
Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol-A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling. PMID:33922473
Interaction of Ligands for PET with the Dopamine D3 Receptor: In Silico and In Vitro Methods. PMID:33918451
Structural Analysis of the Simultaneous Activation and Inhibition of γ-Secretase Activity in the Development of Drugs for Alzheimer's Disease. PMID:33917979
Solution and Membrane Interaction Dynamics of Mycobacterium tuberculosis Fatty Acyl-CoA Synthetase FadD13. PMID:33913324
Structural basis for Clostridium perfringens enterotoxin targeting of claudins at tight junctions in mammalian gut. PMID:33876770
The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. PMID:33854236
The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS model. PMID:33825682
New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells. PMID:33824189
Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance. PMID:33808505
Structure-Activity Relationship of Heterocyclic P2Y14 Receptor Antagonists: Removal of the Zwitterionic Character with Piperidine Bioisosteres. PMID:33787273
Ceramide-1-phosphate transfer protein (CPTP) regulation by phosphoinositides. PMID:33781749
The CFTR P67L variant reveals a key role for N-terminal lasso helices in channel folding, maturation, and pharmacologic rescue. PMID:33781744
How does Sec63 affect the conformation of Sec61 in yeast? PMID:33780447
Design of buried charged networks in artificial proteins. PMID:33767131
Association of sigma-1 receptor with dopamine transporter attenuates the binding of methamphetamine via distinct helix-helix interactions. PMID:33754484
Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. PMID:33753488
Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking. PMID:33739970
Structural and functional analysis of tomato sterol C22 desaturase. PMID:33731007
Prediction of amphipathic helix-membrane interactions with Rosetta. PMID:33730029
An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans. PMID:33720927
N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. PMID:33676924
Decoding the Molecular Effects of Atovaquone Linked Resistant Mutations on Plasmodium falciparum Cytb-ISP Complex in the Phospholipid Bilayer Membrane. PMID:33670016
Structure-based identification of dual ligands at the A2AR and PDE10A with anti-proliferative effects in lung cancer cell-lines. PMID:33658076
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations. PMID:33652554
Structural determinants of cholesterol recognition in helical integral membrane proteins. PMID:33640379
Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs. PMID:33633398
MPBuilder: A PyMOL Plugin for Building and Refinement of Solubilized Membrane Proteins Against Small Angle X-ray Scattering Data. PMID:33631193
Deciphering the Mechanism of Inhibition of SERCA1a by Sarcolipin Using Molecular Simulations. PMID:33614704
De novo design of transmembrane β barrels. PMID:33602829
Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids. PMID:33597295
Cholesterol as a modulator of cannabinoid receptor CB2 signaling. PMID:33580091
How μ-opioid receptor recognizes fentanyl. PMID:33579956
The intrinsically disordered N-terminus of the voltage-dependent anion channel. PMID:33577583
OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PMID:33577557
Residue-by-residue analysis of cotranslational membrane protein integration in vivo. PMID:33554862
Peptides-based vaccine against SARS-nCoV-2 antigenic fragmented synthetic epitopes recognized by T cell and β-cell initiation of specific antibodies to fight the infection. PMID:33552630
Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation. PMID:33547286
Phospholipase iPLA2β averts ferroptosis by eliminating a redox lipid death signal. PMID:33542532
Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter. PMID:33510870
Mycobacterium tuberculosis and M. bovis BCG Moreau Fumarate Reductase Operons Produce Different Polypeptides That May Be Related to Non-canonical Functions. PMID:33510737
Conformational Landscape of Cytochrome P450 Reductase Interactions. PMID:33498551
Glycoconjugate pathway connections revealed by sequence similarity network analysis of the monotopic phosphoglycosyl transferases. PMID:33472976
An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. PMID:33420418
Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers. PMID:33420032
Biased Ligands Differentially Shape the Conformation of the Extracellular Loop Region in 5-HT2B Receptors. PMID:33419260
Structural basis for voltage-sensor trapping of the cardiac sodium channel by a deathstalker scorpion toxin. PMID:33397917
Cryoelectron microscopy structure and mechanism of the membrane-associated electron-bifurcating flavoprotein Fix/EtfABCX. PMID:33372143
A selective transmembrane recognition mechanism by a membrane-anchored ubiquitin ligase adaptor. PMID:33351099
Membrane Proteocomplexome of Campylobacter jejuni Using 2-D Blue Native/SDS-PAGE Combined to Bioinformatics Analysis. PMID:33329413
Distinct GluN1 and GluN2 Structural Determinants for Subunit-Selective Positive Allosteric Modulation of N-Methyl-d-aspartate Receptors. PMID:33326224
How GPCR Phosphorylation Patterns Orchestrate Arrestin-Mediated Signaling. PMID:33296703
Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields. PMID:33295174
Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. PMID:33243981
Phosphatidylglyerol Lipid Binding at the Active Site of an Intramembrane Protease. PMID:33210155
Dimer Organization of Membrane-Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive 1 H-Detected Solid-State NMR. PMID:33205864
Gating-related Structural Dynamics of the MgtE Magnesium Channel in Membrane-Mimetics Utilizing Site-Directed Tryptophan Fluorescence. PMID:33203509
Viral rhodopsins 1 are an unique family of light-gated cation channels. PMID:33177509
Structures and pH-sensing mechanism of the proton-activated chloride channel. PMID:33149300
Subtype-selective mechanisms of negative allosteric modulators binding to group I metabotropic glutamate receptors. PMID:33122823
Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. PMID:33106659
Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes. PMID:33102525
Database resources of the National Center for Biotechnology Information. PMID:33095870
Allosteric mechanism for KCNE1 modulation of KCNQ1 potassium channel activation. PMID:33095155
Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. PMID:33084570
Binding Mode Exploration of B1 Receptor Antagonists' by the Use of Molecular Dynamics and Docking Simulation-How Different Target Engagement Can Determine Different Biological Effects. PMID:33081372
CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae. PMID:33033258
Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2. PMID:32993041
Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity. PMID:32983400
Molecular basis for a new bovine model of Niemann-Pick type C disease. PMID:32970694
Simulation of pH-Dependent, Loop-Based Membrane Protein Gating Using Pretzel. PMID:32918736
Chiral Recognition of Flexible Melatonin Receptor Ligands Induced by Conformational Equilibria. PMID:32899888
Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)-Ligand Binding: A Structural Biology Study Based on Computational Methods. PMID:32875251
Structural basis for the reaction cycle of DASS dicarboxylate transporters. PMID:32869741
Structure of human ATG9A: how holey art thou? PMID:32840139
Evidence that the TRPV1 S1-S4 membrane domain contributes to thermosensing. PMID:32820172
Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms. PMID:32804077
Atomistic structure and dynamics of the human MHC-I peptide-loading complex. PMID:32788370
Mechanisms of Herb-Drug Interactions Involving Cinnamon and CYP2A6: Focus on Time-Dependent Inhibition by Cinnamaldehyde and 2-Methoxycinnamaldehyde. PMID:32788161
Exploration of Alternative Scaffolds for P2Y14 Receptor Antagonists Containing a Biaryl Core. PMID:32787142
Unraveling the complex enzymatic machinery making a key galactolipid in chloroplast membrane: a multiscale computer simulation. PMID:32782311
Conserved Luminal C-Terminal Domain Dynamically Controls Interdomain Communication in Sarcolipin. PMID:32668157
Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. PMID:32649824
Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation. PMID:32632293
Heterologous expression of concatenated nicotinic ACh receptors: Pros and cons of subunit concatenation and recommendations for construct designs. PMID:32627170
Computational structure modeling for diverse categories of macromolecular interactions. PMID:32599506
Structures of metabotropic GABAB receptor. PMID:32580208
Structural insight into the formation of lipoprotein-β-barrel complexes. PMID:32572278
Structural basis of the activation of a metabotropic GABA receptor. PMID:32555460
Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity. PMID:32555203
Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities. PMID:32532023
ELA/APELA precursor cleaved by furin displays tumor suppressor function in renal cell carcinoma through mTORC1 activation. PMID:32516140
Be Cautious with Crystal Structures of Membrane Proteins or Complexes Prepared in Detergents. PMID:32494365
Structures of human pannexin 1 reveal ion pathways and mechanism of gating. PMID:32494015
Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation. PMID:32483232
Deep-AmPEP30: Improve Short Antimicrobial Peptides Prediction with Deep Learning. PMID:32464552
New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies. PMID:32439887
Effect of ethanol on Munc13-1 C1 in Membrane: A Molecular Dynamics Simulation Study. PMID:32424866
An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions. PMID:32415234
A novel theoretical framework reveals more than one voltage-sensing pathway in the lateral membrane of outer hair cells. PMID:32384538
Comparative Analyses of the Conformational Dynamics Between the Soluble and Membrane-Bound Cytokine Receptors. PMID:32366846
Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18. PMID:32365486
Molecular mechanism of light-driven sodium pumping. PMID:32358514
A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. PMID:32332106
PyRod Enables Rational Homology Model-based Virtual Screening Against MCHR1. PMID:32329245
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. PMID:32327568
Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families. PMID:32320418
Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins. PMID:32301705
The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire. PMID:32289252
Membrane mediated toppling mechanism of the folate energy coupling factor transporter. PMID:32273501
Truncated (N)-Methanocarba Nucleosides as Partial Agonists at Mouse and Human A3 Adenosine Receptors: Affinity Enhancement by N6-(2-Phenylethyl) Substitution. PMID:32271569
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. PMID:32224301
NMDA receptor channel gating control by the pre-M1 helix. PMID:32221541
Tracking Ca2+ ATPase intermediates in real time by x-ray solution scattering. PMID:32219166
Combining Molecular Dynamics and Docking Simulations to Develop Targeted Protocols for Performing Optimized Virtual Screening Campaigns on The hTRPM8 Channel. PMID:32218173
Cardiovascular response to small-molecule APJ activation. PMID:32208384
Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes. PMID:32205149
Ste24: An Integral Membrane Protein Zinc Metalloprotease with Provocative Structure and Emergent Biology. PMID:32199981
Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. PMID:32189026
Site-specific functionality and tryptophan mimicry of lipidation in tetraspanin CD9. PMID:32181977
Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity. PMID:32168319
Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches. PMID:32164183
Structure-Function Studies and Mechanism of Action of Snake Venom L-Amino Acid Oxidases. PMID:32158389
The structural study of mutation-induced inactivation of human muscarinic receptor M4. PMID:32148857
Computer simulations of protein-membrane systems. PMID:32145948
Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). PMID:32134653
Analysis of protein missense alterations by combining sequence- and structure-based methods. PMID:32096919
Localized Axolemma Deformations Suggest Mechanoporation as Axonal Injury Trigger. PMID:32082244
Replacing the eleven native tryptophans by directed evolution produces an active P-glycoprotein with site-specific, non-conservative substitutions. PMID:32081894
The Ca2+ permeation mechanism of the ryanodine receptor revealed by a multi-site ion model. PMID:32066742
Evolutionary aspects and enzymology of metazoan carotenoid cleavage oxygenases. PMID:32061750
Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling. PMID:32060286
GPR6 Structural Insights: Homology Model Construction and Docking Studies. PMID:32046081
High-resolution structural insights into the heliorhodopsin family. PMID:32034096
β11-12 linker isomerization governs acid-sensing ion channel desensitization and recovery. PMID:32031522
Intracellular Delivery of DNA and Protein by a Novel Cell-Permeable Peptide Derived from DOT1L. PMID:32024261
Structural Changes of Sarco/Endoplasmic Reticulum Ca2+-ATPase Induced by Rutin Arachidonate: A Molecular Dynamics Study. PMID:32024167
Structure-guided discovery of a single-domain antibody agonist against human apelin receptor. PMID:31998837
Surface Plasmon Resonance as a Tool for Ligand Binding Investigation of Engineered GPR17 Receptor, a G Protein Coupled Receptor Involved in Myelination. PMID:31998697
Assessing Structural Determinants of Zn2+ Binding to Human HV1 via Multiple MD Simulations. PMID:31972155
Conformational changes in Apolipoprotein N-acyltransferase (Lnt). PMID:31959792
Insertion of Bacteriorhodopsin Helix C Variants into Biological Membranes. PMID:31956802
Structure of the M2 muscarinic receptor-β-arrestin complex in a lipid nanodisc. PMID:31945772
Comparative modeling and docking of chemokine-receptor interactions with Rosetta. PMID:31924303
A bipartite structural organization defines the SERINC family of HIV-1 restriction factors. PMID:31907454
A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures. PMID:31892539
The Significance of Halogen Bonding in Ligand-Receptor Interactions: The Lesson Learned from Molecular Dynamic Simulations of the D4 Receptor. PMID:31881785
Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB. PMID:31881208
Molecular basis of force-from-lipids gating in the mechanosensitive channel MscS. PMID:31880537
A Strategic Approach for Fluorescence Imaging of Membrane Proteins in a Native-like Environment. PMID:31831268
Novel FSHR variants causing female resistant ovary syndrome. PMID:31830376
Unusual features of the c-ring of F1FO ATP synthases. PMID:31811229
Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors. PMID:31811124
Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. PMID:31776516
Phospholipid Component Defines Pharmacokinetic and Pharmacodynamic Properties of Synthetic High-Density Lipoproteins. PMID:31776208
Multidrug Resistance in Neisseria gonorrhoeae: Identification of Functionally Important Residues in the MtrD Efflux Protein. PMID:31744915
Alterations in plasma membrane ion channel structures stimulate NLRP3 inflammasome activation in APOL1 risk milieu. PMID:31714001
Mutagenesis facilitated crystallization of GLP-1R. PMID:31709055
Intranasal Peptide-Based FpvA-KLH Conjugate Vaccine Protects Mice From Pseudomonas aeruginosa Acute Murine Pneumonia. PMID:31708925
In silico characterization of residues essential for substrate binding of human cystine transporter, xCT. PMID:31705320
Feedforward Control of Plant Nitrate Transporter NRT1.1 Biphasic Adaptive Activity. PMID:31699333
Covalently modified carboxyl side chains on cell surface leads to a novel method toward topology analysis of transmembrane proteins. PMID:31673029
Unique structure and function of viral rhodopsins. PMID:31666521
Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores. PMID:31664022
The tripartite architecture of the eukaryotic integral membrane protein zinc metalloprotease Ste24. PMID:31644822
Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs. PMID:31633023
Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state. PMID:31624123
Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. PMID:31605097
Allosteric activation of an ion channel triggered by modification of mechanosensitive nano-pockets. PMID:31601809
On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations. PMID:31587831
Intracellular cholesterol trafficking is dependent upon NPC2 interaction with lysobisphosphatidic acid. PMID:31580258
The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development. PMID:31560649
Upgraded molecular models of the human KCNQ1 potassium channel. PMID:31518351
Identification of 4-Amino-Thieno[2,3-d]Pyrimidines as QcrB Inhibitors in Mycobacterium tuberculosis. PMID:31511370
A Molecular Dynamics Study of Vasoactive Intestinal Peptide Receptor 1 and the Basis of Its Therapeutic Antagonism. PMID:31491880
Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1. PMID:31481523
Insights into the ZIKV NS1 Virology from Different Strains through a Fine Analysis of Physicochemical Properties. PMID:31458257
Improved homology modeling of the human & rat EP4 prostanoid receptors. PMID:31455205
A comprehensive computational study of amino acid interactions in membrane proteins. PMID:31427701
Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens. PMID:31417509
Universal principles of membrane protein assembly, composition and evolution. PMID:31415673
The ghrelin O-acyltransferase structure reveals a catalytic channel for transmembrane hormone acylation. PMID:31413115
Secretory Phospholipases A2 in Plants. PMID:31354755
Presence of substrate aids lateral gate separation in LptD. PMID:31351059
Bacterial outer membrane proteins assemble via asymmetric interactions with the BamA β-barrel. PMID:31350400
Tryptophan Oxidation in the UQCRC1 Subunit of Mitochondrial Complex III (Ubiquinol-Cytochrome C Reductase) in a Mouse Model of Myodegeneration Causes Large Structural Changes in the Complex: A Molecular Dynamics Simulation Study. PMID:31337785
Cannabidiol binding and negative allosteric modulation at the cannabinoid type 1 receptor in the presence of delta-9-tetrahydrocannabinol: An In Silico study. PMID:31335889
Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture. PMID:31316715
Benchmarking subcellular localization and variant tolerance predictors on membrane proteins. PMID:31307390
Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking. PMID:31303974
Enhanced agonist residence time, internalization rate and signalling of the GIP receptor variant [E354Q] facilitate receptor desensitization and long-term impairment of the GIP system. PMID:31299132
MemBlob database and server for identifying transmembrane regions using cryo-EM maps. PMID:31290936
A structural model of the human serotonin transporter in an outward-occluded state. PMID:31251747
MolMeDB: Molecules on Membranes Database. PMID:31250015
Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR. PMID:31249143
Identification of a Novel Allosteric Modulator of the Human Dopamine Transporter. PMID:31184115
Interaction of the Mechanosensitive Channel, MscS, with the Membrane Bilayer through Lipid Intercalation into Grooves and Pockets. PMID:31173776
Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. PMID:31147549
Synthesis, Biological Evaluation, and Molecular Modeling Studies of New Thiadiazole Derivatives as Potent P2X7 Receptor Inhibitors. PMID:31134177
Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions. PMID:31107861
Structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis. PMID:31098408
Towards A Molecular Understanding of The Cannabinoid Related Orphan Receptor GPR18: A Focus on Its Constitutive Activity. PMID:31075933
Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB. PMID:31070373
Structure and Dynamics of the Central Lipid Pool and Proteins of the Bacterial Holo-Translocon. PMID:31053257
Novel 3,4-Dihydroisocoumarins Inhibit Human P-gp and BCRP in Multidrug Resistant Tumors and Demonstrate Substrate Inhibition of Yeast Pdr5. PMID:31040786
Recent advances in computational studies of GPCR-G protein interactions. PMID:31036298
Comparative docking analysis of cholesterol analogs to ion channels to discriminate between stereospecific binding vs. stereospecific response. PMID:31033379
Role of Second Quinone Binding Site in Proton Pumping by Respiratory Complex I. PMID:31024903
Structural basis of ligand recognition at the human MT1 melatonin receptor. PMID:31019306
Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. PMID:31019304
A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes. PMID:31013635
Structure and mechanisms of sodium-pumping KR2 rhodopsin. PMID:30989112
Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. PMID:30978005
Does the Lipid Bilayer Orchestrate Access and Binding of Ligands to Transmembrane Orthosteric/Allosteric Sites of G Protein-Coupled Receptors? PMID:30967440
A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods. PMID:30934701
Computer aided protein engineering to enhance the thermo-stability of CXCR1- T4 lysozyme complex. PMID:30926935
X-Ray Structure of Human Sulfide:Quinone Oxidoreductase: Insights into the Mechanism of Mitochondrial Hydrogen Sulfide Oxidation. PMID:30905673
Conserved Residues Control the T1R3-Specific Allosteric Signaling Pathway of the Mammalian Sweet-Taste Receptor. PMID:30893427
Dopamine D4 Receptor-Selective Compounds Reveal Structure-Activity Relationships that Engender Agonist Efficacy. PMID:30883109
Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR. PMID:30850624
Septin 9 has Two Polybasic Domains Critical to Septin Filament Assembly and Golgi Integrity. PMID:30831549
Volta Phase Plate Cryo-EM Structure of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2. PMID:30795505
Lipid⁻Protein Interactions in Niemann⁻Pick Type C Disease: Insights from Molecular Modeling. PMID:30736449
Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis. PMID:30718392
New insights into GluT1 mechanics during glucose transfer. PMID:30700737
γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding. PMID:30662893
Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function. PMID:30658838
Understanding Membrane Domain-Partitioning Thermodynamics of Transmembrane Domains with Potential of Mean Force Calculations. PMID:30638009
Design and in Vivo Characterization of A1 Adenosine Receptor Agonists in the Native Ribose and Conformationally Constrained (N)-Methanocarba Series. PMID:30605331
Mammalian class I odorant receptors exhibit a conserved vestibular-binding pocket. PMID:30599066
Genome Mining of Plant NPFs Reveals Varying Conservation of Signature Motifs Associated With the Mechanism of Transport. PMID:30564251
Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor. PMID:30510194
Binding of histamine to the H1 receptor-a molecular dynamics study. PMID:30498974
Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. PMID:30449325
Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP. PMID:30448037
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. PMID:30418645
A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations. PMID:30413241
Role of the Fractalkine Receptor in CNS Autoimmune Inflammation: New Approach Utilizing a Mouse Model Expressing the Human CX3CR1I249/M280 Variant. PMID:30386211
The extracellular loop of Man-PTS subunit IID is responsible for the sensitivity of Lactococcus garvieae to garvicins A, B and C. PMID:30361679
EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins. PMID:30357403
Monotopic Membrane Proteins Join the Fold. PMID:30337134
Promiscuous attraction of ligands within the ATP binding site of RyR2 promotes diverse gating behaviour. PMID:30301919
The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin. PMID:30287110
Exploring the Ligand Efficacy of Cannabinoid Receptor 1 (CB1) using Molecular Dynamics Simulations. PMID:30213978
Small membranous proteins of the TorE/NapE family, crutches for cognate respiratory systems in Proteobacteria. PMID:30206249
Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics. PMID:30200318
In silico Description of LAT1 Transport Mechanism at an Atomistic Level. PMID:30197880
Insights into the key determinants of membrane protein topology enable the identification of new monotopic folds. PMID:30168796
US28: HCMV's Swiss Army Knife. PMID:30127279
Inward- and outward-facing homology modeling of human concentrative nucleoside transporter 3 (hCNT3) predicts an elevator-type transport mechanism. PMID:30096006
C-terminal kink formation is required for lateral gating in BamA. PMID:30087180
Calcium is an essential cofactor for metal efflux by the ferroportin transporter family. PMID:30082682
Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins. PMID:30063209
A model for hydrophobic protrusions on peripheral membrane proteins. PMID:30048443
Inward-facing conformation of l-ascorbate transporter suggests an elevator mechanism. PMID:30038796
Mapping the sensing spots of aerolysin for single oligonucleotides analysis. PMID:30026547
Lipid Bilayer Interactions of Amyloidogenic N-Terminal Fragment of Apolipoprotein A-I Probed by Förster Resonance Energy Transfer and Molecular Dynamics Simulations. PMID:30008060
Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell. PMID:30001212
Effect of Site-Specific Intermolecular Lysine-Tryptophan Interactions on the Aggregation of Gramicidin-Based Peptides Leading to Pore Formation in Lipid Membranes. PMID:29995247
The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase. PMID:29925590
Scavenging of superoxide by a membrane-bound superoxide oxidase. PMID:29915379
Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa. PMID:29910784
Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. PMID:29883591
Extrinsic Tryptophans as NMR Probes of Allosteric Coupling in Membrane Proteins: Application to the A2A Adenosine Receptor. PMID:29874058
Structure-based analysis of CysZ-mediated cellular uptake of sulfate. PMID:29792261
Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. PMID:29728606
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). PMID:29718451
On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation. PMID:29636500
A Mechanism of Calmodulin Modulation of the Human Cardiac Sodium Channel. PMID:29606593
Structural mechanisms of CFTR function and dysfunction. PMID:29581173
Cytochrome aa3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O2 for Catalysis. PMID:29546752
Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins. PMID:29535329
Mechanisms of KCNQ1 channel dysfunction in long QT syndrome involving voltage sensor domain mutations. PMID:29532034
Disease-associated missense mutations in GluN2B subunit alter NMDA receptor ligand binding and ion channel properties. PMID:29511171
Structure and mechanogating mechanism of the Piezo1 channel. PMID:29469092
Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. PMID:29427530
Pseudomonas pseudoalcaligenes KF707 grown with biphenyl expresses a cytochrome caa3 oxidase that uses cytochrome c4 as electron donor. PMID:29427514
Solution structure and elevator mechanism of the membrane electron transporter CcdA. PMID:29379172
Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. PMID:29319301
Cripto stabilizes GRP78 on the cell membrane. PMID:29226519
The P-type ATPase CtpG preferentially transports Cd2+ across the Mycobacterium tuberculosis plasma membrane. PMID:29197950
Computational insights into the G-protein-biased activation and inactivation mechanisms of the μ opioid receptor. PMID:29188799
Structural insights into the committed step of bacterial phospholipid biosynthesis. PMID:29167463
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. PMID:29155578
Structure-function relationships in ABCG2: insights from molecular dynamics simulations and molecular docking studies. PMID:29138424
Computational design of membrane proteins using RosettaMembrane. PMID:29090504
Structure and Membrane Topography of the Vibrio-Type Secretin Complex from the Type 2 Secretion System of Enteropathogenic Escherichia coli. PMID:29084860
Structural, physicochemical and dynamic features conserved within the aerolysin pore-forming toxin family. PMID:29066778
Computational insights into the subtype selectivity and "message-address-efficacy" mechanisms of opioid receptors through JDTic binding and unbinding. PMID:29047460
ChannelsDB: database of biomacromolecular tunnels and pores. PMID:29036719
Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1. PMID:28978444
Negatively charged residues in the first extracellular loop of the L-type CaV1.2 channel anchor the interaction with the CaVα2δ1 auxiliary subunit. PMID:28864774
A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations. PMID:28863193
A membrane-inserted structural model of the yeast mitofusin Fzo1. PMID:28860650
Cysteines and N-Glycosylation Sites Conserved among All Alphaherpesviruses Regulate Membrane Fusion in Herpes Simplex Virus 1 Infection. PMID:28835497
Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters. PMID:28808284
Targeting P-glycoprotein: Investigation of piperine analogs for overcoming drug resistance in cancer. PMID:28801675
In silico model of the human ClC-Kb chloride channel: pore mapping, biostructural pathology and drug screening. PMID:28775266
Impact of LCA-Associated E14L LRAT Mutation on Protein Stability and Retinoid Homeostasis. PMID:28758396
Machine learning-enabled discovery and design of membrane-active peptides. PMID:28728899
Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle. PMID:28718450
Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer. PMID:28702543
Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase. PMID:28648609
Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport. PMID:28630154
Identification of the gene that codes for the σ2 receptor. PMID:28559337
Fast iodide-SAD phasing for high-throughput membrane protein structure determination. PMID:28508075
Protein-phospholipid interplay revealed with crystals of a calcium pump. PMID:28467821
Peripheral membrane associations of matrix metalloproteinases. PMID:28442379
Substituted cysteine accessibility method (SCAM) analysis of the transport domain of human concentrative nucleoside transporter 3 (hCNT3) and other family members reveals features of structural and functional importance. PMID:28385889
Distinct domains of the β1-subunit cytosolic N terminus control surface expression and functional properties of large-conductance calcium-activated potassium (BK) channels. PMID:28373283
TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer. PMID:28365741
Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae. PMID:28324524
Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. PMID:28324295
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. PMID:28219343
Quantification of Detergents Complexed with Membrane Proteins. PMID:28176812
Accessing gap-junction channel structure-function relationships through molecular modeling and simulations. PMID:28124624
Functional Characterization of the N-Terminal C2 Domain from Arabidopsis thaliana Phospholipase Dα and Dβ. PMID:28101506
Conformational Transitions and Alternating-Access Mechanism in the Sarcoplasmic Reticulum Calcium Pump. PMID:28093226
Structure-Based Scaffold Repurposing for G Protein-Coupled Receptors: Transformation of Adenosine Derivatives into 5HT2B/5HT2C Serotonin Receptor Antagonists. PMID:27933810
Three-dimensional Modelling of the Voltage-gated Sodium Ion Channel from Anopheles gambiae Reveals Spatial Clustering of Evolutionarily Conserved Acidic Residues at the Extracellular Sites. PMID:27919210
Data on diverse roles of helix perturbations in membrane proteins. PMID:27844046
Antiplasmodial Activity Is an Ancient and Conserved Feature of Tick Defensins. PMID:27822206
Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains. PMID:27814978
A novel approach using C. elegans DNA damage-induced apoptosis to characterize the dynamics of uptake transporters for therapeutic drug discoveries. PMID:27786254
Nematode Peptides with Host-Directed Anti-inflammatory Activity Rescue Caenorhabditis elegans from a Burkholderia pseudomallei Infection. PMID:27672387
Structure of the STRA6 receptor for retinol uptake. PMID:27563101
Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif. PMID:27554809
Split-ubiquitin yeast two-hybrid interaction reveals a novel interaction between a natural resistance associated macrophage protein and a membrane bound thioredoxin in Brassica juncea. PMID:27534419
Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier. PMID:27532224
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
A conserved amino acid residue critical for product and substrate specificity in plant triterpene synthases. PMID:27412861
Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin. PMID:27320406
Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F. PMID:27276259
New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies. PMID:27226570
Crystal structure of the human σ1 receptor. PMID:27042935
Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. PMID:26912703
Molecular switches of the κ opioid receptor triggered by 6'-GNTI and 5'-GNTI. PMID:26742690
The Crystal Structure of an Integral Membrane Fatty Acid α-Hydroxylase. PMID:26515067
Rosuvastatin Alters the Proteome of High Density Lipoproteins: Generation of alpha-1-antitrypsin Enriched Particles with Anti-inflammatory Properties. PMID:26483418
Pathways and Barriers for Ion Translocation through the 5-HT3A Receptor Channel. PMID:26465896
Determining the N-terminal orientations of recombinant transmembrane proteins in the Escherichia coli plasma membrane. PMID:26462555
Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB. PMID:26365278
An Integrated Framework Advancing Membrane Protein Modeling and Design. PMID:26325167
TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. PMID:26289158
STARD4 Membrane Interactions and Sterol Binding. PMID:26168008
Expression and Characterization of the Novel Gene fr47 during Freezing in the Wood Frog, Rana sylvatica. PMID:26101667
MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. PMID:26073602
Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. PMID:25998378
Comparative modeling of hypothetical amyloid pores based on cylindrin. PMID:25994458
A hydrophobic proline-rich motif is involved in the intracellular targeting of temperature-induced lipocalin. PMID:25957952
Structure of the Angiotensin receptor revealed by serial femtosecond crystallography. PMID:25913193
CHEXVIS: a tool for molecular channel extraction and visualization. PMID:25888118
High-resolution structure of a type IV pilin from the metal-reducing bacterium Shewanella oneidensis. PMID:25886849
The composition of the global and feature specific cyanobacterial core-genomes. PMID:25852675
Crystal structure of a light-driven sodium pump. PMID:25849142
Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering. PMID:25833378
The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions. PMID:25703378
Looking into laminin receptor: critical discussion regarding the non-integrin 37/67-kDa laminin receptor/RPSA protein. PMID:25630983
Molecular determinants of α-synuclein mutants' oligomerization and membrane interactions. PMID:25561023
Sites and functional consequence of VDAC-alkylphenol anesthetic interactions. PMID:25448677
New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. PMID:25408848
Expediting topology data gathering for the TOPDB database. PMID:25392424
Computational modeling of membrane proteins. PMID:25355688
Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics. PMID:25287046
ProBLM web server: protein and membrane placement and orientation package. PMID:25126110
A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa. PMID:25084326
Computational investigation of cholesterol binding sites on mitochondrial VDAC. PMID:25080204
Cell-free expression and in meso crystallisation of an integral membrane kinase for structure determination. PMID:25012698
Revisiting the structure of the Vps10 domain of human sortilin and its interaction with neurotensin. PMID:24985322
Life at the border: adaptation of proteins to anisotropic membrane environment. PMID:24947665
Structural characterization of human cholesterol 7α-hydroxylase. PMID:24927729
Structural basis for catalysis in a CDP-alcohol phosphotransferase. PMID:24923293
Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. PMID:24688707
Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2. PMID:24419389
ERAD and protein import defects in a sec61 mutant lacking ER-lumenal loop 7. PMID:24314051
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. PMID:24302577
A novel membrane sensor controls the localization and ArfGEF activity of bacterial RalF. PMID:24244168
Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation. PMID:24240640
MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins. PMID:24194596
Membrane protein orientation and refinement using a knowledge-based statistical potential. PMID:24047460
Identification of cysteine residues in human cationic amino acid transporter hCAT-2A that are targets for inhibition by N-ethylmaleimide. PMID:24019517
Host Lipid and Temperature as Important Screening Variables for Crystallizing Integral Membrane Proteins in Lipidic Mesophases. Trials with Diacylglycerol Kinase. PMID:23956688
Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding. PMID:23927370
Structure of the human glucagon class B G-protein-coupled receptor. PMID:23863937
Structural model of the anion exchanger 1 (SLC4A1) and identification of transmembrane segments forming the transport site. PMID:23846695
Structural adaptations of proteins to different biological membranes. PMID:23811361
Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization. PMID:23785532
Structural basis for alternating access of a eukaryotic calcium/proton exchanger. PMID:23685453
Crystal structure of the integral membrane diacylglycerol kinase. PMID:23676677
Membrane phospholipid bilayer as a determinant of monoacylglycerol lipase kinetic profile and conformational repertoire. PMID:23553709
Crystal structure of a eukaryotic phosphate transporter. PMID:23542591
Structural features for functional selectivity at serotonin receptors. PMID:23519215
Structure of the trypanosome cyanide-insensitive alternative oxidase. PMID:23487766
Centralspindlin links the mitotic spindle to the plasma membrane during cytokinesis. PMID:23235882
PDBTM: Protein Data Bank of transmembrane proteins after 8 years. PMID:23203988
Structure of the type III secretion effector protein ExoU in complex with its chaperone SpcU. PMID:23166655
Crystal structure of a voltage-gated K+ channel pore module in a closed state in lipid membranes. PMID:23095758
Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing. PMID:22984481
Tetrameric structure of the GlfT2 galactofuranosyltransferase reveals a scaffold for the assembly of mycobacterial Arabinogalactan. PMID:22707726
A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism. PMID:22692182
Structure-based statistical analysis of transmembrane helices. PMID:22588483
Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. PMID:22579257
Emerging methodologies to investigate lipid-protein interactions. PMID:22327461
https://doi.org/10.1016/j.future.2010.07.005
http://dx.doi.org/10.1093/nar/GKR703

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resource metadata
metasource: Fairsharing.org
version: None

structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

membrane and lipoproteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.335215

resource metadata structure protein structure protein folds and structural domains membrane and lipoproteins small molecule proteins

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Manually Curated Database of Rice Proteins