MolMovDB

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MolMovDB

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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molmovdb

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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Other names: molmovdb

The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.

Webpage:

Publications:

Publications

More detailed information about this field from each metasource. ×

MolMovDB: analysis and visualization of conformational change and structural flexibility
PMID: 12520056

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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• MolMovDB: analysis and visualization of conformational change and structural flexibility PubMed citations: 65.

  65 articles citing: MolMovDB: analysis and visualization of conformational change and structural flexibility

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  D3PM: a comprehensive database for protein motions ranging from residue to domain. PMID:35164668

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  "Protein" no longer means what it used to. PMID:34308370

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  Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. PMID:33961840

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  Predicting Protein Functional Motions: an Old Recipe with a New Twist. PMID:32330413

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  Considerations on the Rational Design of Covalently Conjugated Cell-Penetrating Peptides (CPPs) for Intracellular Delivery of Proteins: A Guide to CPP Selection Using Glucarpidase as the Model Cargo Molecule. PMID:31779220

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  ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths. PMID:31435895

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  Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PMID:30699115

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  Generating conformational transition paths with low potential-energy barriers for proteins. PMID:30069648

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  Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank. PMID:29103094

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  Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change. PMID:28445748

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  Knowledge-based entropies improve the identification of native protein structures. PMID:28265078

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  Single molecule optical measurements of orientation and rotations of biological macromolecules. PMID:28192292

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  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PMID:27124275

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  CCProf: exploring conformational change profile of proteins. PMID:27016699

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  iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. PMID:26582920

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  Parsimony in Protein Conformational Change. PMID:26095029

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  Solution structure of a designed cyclic peptide ligand for nickel and copper ions. PMID:25414527

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  Polyphony: superposition independent methods for ensemble-based drug discovery. PMID:25265915

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  A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity. PMID:24789327

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  MORPH-PRO: a novel algorithm and web server for protein morphing. PMID:23844614

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  VLDP web server: a powerful geometric tool for analysing protein structures in their environment. PMID:23761450

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  X-ray structure of the mammalian GIRK2-βγ G-protein complex. PMID:23739333

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  Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. PMID:23682200

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  PheVI:09 (Phe6.44) as a sliding microswitch in seven-transmembrane (7TM) G protein-coupled receptor activation. PMID:23135271

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  Structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase. PMID:23012373

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  The KCNE Tango - How KCNE1 Interacts with Kv7.1. PMID:22876232

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  Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel. PMID:22678295

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  Towards the prediction of order parameters from molecular dynamics simulations in proteins. PMID:22559464

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  Open structure of the Ca2+ gating ring in the high-conductance Ca2+-activated K+ channel. PMID:22139424

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  Predicting protein flexibility through the prediction of local structures. PMID:21287616

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  Computing ensembles of transitions from stable states: Dynamic importance sampling. PMID:21132840

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  Molecular basis of BACH1/FANCJ recognition by TopBP1 in DNA replication checkpoint control. PMID:21127055

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  Information Visualization Techniques in Bioinformatics during the Postgenomic Era. PMID:20976032

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  Using diffusion distances for flexible molecular shape comparison. PMID:20868474

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  Prediction of protein motions from amino acid sequence and its application to protein-protein interaction. PMID:20626880

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  Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability. PMID:20469886

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  Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein. PMID:20141110

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  Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. PMID:19591676

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  IDSS: deformation invariant signatures for molecular shape comparison. PMID:19463181

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  Three dimensional shape comparison of flexible proteins using the local-diameter descriptor. PMID:19435524

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  Rapid sampling of molecular motions with prior information constraints. PMID:19247429

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  Using least median of squares for structural superposition of flexible proteins. PMID:19159484

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  Generation, comparison, and merging of pathways between protein conformations: gating in K-channels. PMID:18621834

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  The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates. PMID:18346970

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  Matt: local flexibility aids protein multiple structure alignment. PMID:18193941

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  Sequence-similar, structure-dissimilar protein pairs in the PDB. PMID:18004789

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  Comparative analysis of protein structure alignments. PMID:17672887

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  TMM@: a web application for the analysis of transmembrane helix mobility. PMID:17601351

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  The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. PMID:17263143

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  Docking protein domains in contact space. PMID:16790041

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  Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. PMID:16565070

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  A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure. PMID:16552141

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  Assessing local structural perturbations in proteins. PMID:16159393

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  Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. PMID:16145054

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  A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein. PMID:16143635

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  Coarse-grained normal mode analysis in structural biology. PMID:16143512

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  Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. PMID:16087736

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  Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. PMID:16061186

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  Structure-based engineering of internal cavities in coiled-coil peptides. PMID:16008357

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  iGNM: a database of protein functional motions based on Gaussian Network Model. PMID:15860562

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  WEBnm@: a web application for normal mode analyses of proteins. PMID:15762993

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  Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. PMID:15722444

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  How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation. PMID:15240452

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  Acetyl-coenzyme A synthase: the case for a Ni(p)(0)-based mechanism of catalysis. PMID:15221478

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  Transconformations of the SERCA1 Ca-ATPase: a normal mode study. PMID:14507684

Tags:

Tags

More detailed information about this field from each metasource. ×

nucleic acid structure analysis

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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molecular dynamics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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structure prediction

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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structure analysis

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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proteins

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:23.247005

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nucleic acid structure analysis molecular dynamics structure prediction structure analysis proteins