Protein Model Portal
Other names: protein_model_portal
Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. PMP has reached its end of life and no longer provides data.
Description
More detailed information about this field from each metasource.
Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. PMP has reached its end of life and no longer provides data.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:58.650893
Webpage:
https://www.proteinmodelportal.orgWebpage
More detailed information about this field from each metasource.
https://www.proteinmodelportal.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:58.650893
Publications:
Publications
More detailed information about this field from each metasource.
The Protein Model Portal--a comprehensive resource for protein structure and model information
PMID: 23624946
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:58.650893
Publications
More detailed information about this field from each metasource.
The Protein Model Portal--a comprehensive resource for protein structure and model information
PMID: 23624946
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:58.650893
-
The Protein Model Portal--a comprehensive resource for protein structure and model information
PubMed citations: 138.
138 articles citing: The Protein Model Portal--a comprehensive resource for protein structure and model information
Deep learning geometrical potential for high-accuracy ab initio protein structure prediction. PMID:35663033
A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models. PMID:35324806
Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential. PMID:35139120
Secondary structure specific simpler prediction models for protein backbone angles. PMID:34983370
New system for archiving integrative structures. PMID:34866606
The AlphaFold Database of Protein Structures: A Biologist's Guide. PMID:34757056
Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network. PMID:34702851
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. PMID:34137435
Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14. PMID:34035363
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PMID:33770072
Improved Protein Model Quality Assessment By Integrating Sequential And Pairwise Features Using Deep Learning. PMID:33325480
Enhancing protein backbone angle prediction by using simpler models of deep neural networks. PMID:33173130
Predicting binding sites from unbound versus bound protein structures. PMID:32985584
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
Dark Proteome Database: Studies on Disorder. PMID:32629790
Protein Contact Map Prediction Based on ResNet and DenseNet. PMID:32337273
Machine Learning Approaches for Quality Assessment of Protein Structures. PMID:32316682
Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PMID:32295225
Immunoinformatics and Vaccine Development: An Overview. PMID:32161726
Exploring the computational methods for protein-ligand binding site prediction. PMID:32140203
SGID: a comprehensive and interactive database of the silkworm. PMID:31836898
Molecular replacement using structure predictions from databases. PMID:31793899
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). PMID:31633216
The association between TNP2 gene polymorphisms and Iranian infertile men with varicocele: A case-control study. PMID:31583373
Improved homology modeling of the human & rat EP4 prostanoid receptors. PMID:31455205
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. PMID:31427836
A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation. PMID:31401411
Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13. PMID:31292988
Arming oHSV with ULBP3 drives abscopal immunity in lymphocyte-depleted glioblastoma. PMID:31292299
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
The Selective Rat Toxicant Norbormide Blocks KATP Channels in Smooth Muscle Cells But Not in Insulin-Secreting Cells. PMID:31191321
Principles for Integrative Structural Biology Studies. PMID:31150619
Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes. PMID:31148576
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
Dark Proteome Database: Studies on Dark Proteins. PMID:30934744
Anticipating innovations in structural biology. PMID:30912485
Protein structure prediction. PMID:30853739
Small Molecule Docking of DNA Repair Proteins Associated with Cancer Survival Following PCNA Metagene Adjustment: A Potential Novel Class of Repair Inhibitors. PMID:30759820
Privileged Structures and Polypharmacology within and between Protein Families. PMID:30613326
Protein structure networks provide insight into active site flexibility in esterase/lipases from the carnivorous plant Drosera capensis. PMID:30516771
Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2. PMID:30375376
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. PMID:30239678
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. PMID:30109435
A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction. PMID:30087916
PredMP: a web server for de novo prediction and visualization of membrane proteins. PMID:30084960
Molecular docking and pharmacological/toxicological assessment of a new compound designed from celecoxib and paracetamol by molecular hybridization. PMID:30039481
Transcriptional and Translational Landscape of Equine Torovirus. PMID:29950409
Electrostatic Tuning of a Potassium Channel in Electric Fish. PMID:29937349
Protein alignment based on higher order conditional random fields for template-based modeling. PMID:29856860
COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. PMID:29846643
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. PMID:29796670
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
The first case of NSHL by direct impression on EYA1 gene and identification of one novel mutation in MYO7A in the Iranian families. PMID:29511501
Protein homology model refinement by large-scale energy optimization. PMID:29507254
Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks. PMID:29275173
Computational Studies of Snake Venom Toxins. PMID:29271884
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. PMID:29206185
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12. PMID:29178137
LIBRA-WA: a web application for ligand binding site detection and protein function recognition. PMID:29126218
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
The NSAID allosteric site of human cytosolic sulfotransferases. PMID:29038294
Guidelines for the use of flow cytometry and cell sorting in immunological studies. PMID:29023707
Folding Membrane Proteins by Deep Transfer Learning. PMID:28957654
Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. PMID:28913931
Antiproliferative factor (APF) binds specifically to sites within the cytoskeleton-associated protein 4 (CKAP4) extracellular domain. PMID:28893174
AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling. PMID:28884168
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. PMID:28874689
Analysis of deep learning methods for blind protein contact prediction in CASP12. PMID:28845538
Bradyrhizobium elkanii nod regulon: insights through genomic analysis. PMID:28767122
The Dark Proteome Database. PMID:28736578
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models. PMID:28460136
WDR23 regulates NRF2 independently of KEAP1. PMID:28453520
GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure. PMID:28387820
Comparing co-evolution methods and their application to template-free protein structure prediction. PMID:28171606
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. PMID:28150250
Protein Bioinformatics Databases and Resources. PMID:28150231
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PMID:28056090
Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis. PMID:28040565
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. PMID:28035027
Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. PMID:27991516
Replication Protein A Presents Canonical Functions and Is Also Involved in the Differentiation Capacity of Trypanosoma cruzi. PMID:27984589
The SWISS-MODEL Repository-new features and functionality. PMID:27899672
PRIMO: An Interactive Homology Modeling Pipeline. PMID:27855192
Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2. PMID:27796781
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. PMID:27766851
ProQ3: Improved model quality assessments using Rosetta energy terms. PMID:27698390
A Novel Role for Progesterone Receptor Membrane Component 1 (PGRMC1): A Partner and Regulator of Ferrochelatase. PMID:27599036
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. PMID:27587688
Pharmacological targeting of the PDGF-CC signaling pathway for blood-brain barrier restoration in neurological disorders. PMID:27524729
Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms. PMID:27513851
The archiving and dissemination of biological structure data. PMID:27450113
Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. PMID:27378301
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. PMID:27319297
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. PMID:27307635
Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking. PMID:27242194
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. PMID:27190006
Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models. PMID:27149620
CoinFold: a web server for protein contact prediction and contact-assisted protein folding. PMID:27112569
Phylogenetic analysis of β-xylanase SRXL1 of Sporisorium reilianum and its relationship with families (GH10 and GH11) of Ascomycetes and Basidiomycetes. PMID:27040368
MreB-Dependent Organization of the E. coli Cytoplasmic Membrane Controls Membrane Protein Diffusion. PMID:26958890
The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response. PMID:26863566
ProQ2: estimation of model accuracy implemented in Rosetta. PMID:26733453
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
Protein Structure and Function Prediction Using I-TASSER. PMID:26678386
Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. PMID:26677056
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Unexpected features of the dark proteome. PMID:26578815
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. PMID:26545824
MECP2 missense mutations outside the canonical MBD and TRD domains in males with intellectual disability. PMID:26490184
Antisera Against Certain Conserved Surface-Exposed Peptides of Nontypeable Haemophilus influenzae Are Protective. PMID:26390432
ABCB4 mutations in adult patients with cholestatic liver disease: impact and phenotypic expression. PMID:26324191
Dynamic profiling of double-stranded RNA binding proteins. PMID:26184879
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. PMID:26095030
Building a virtual ligand screening pipeline using free software: a survey. PMID:26094053
Novel Drug Targets for Food-Borne Pathogen Campylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study. PMID:26061459
RBO Aleph: leveraging novel information sources for protein structure prediction. PMID:25897112
I-TASSER server: new development for protein structure and function predictions. PMID:25883148
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences. PMID:25820431
Discovery of novel new Delhi metallo-β-lactamases-1 inhibitors by multistep virtual screening. PMID:25734558
Data to knowledge: how to get meaning from your result. PMID:25610627
The I-TASSER Suite: protein structure and function prediction. PMID:25549265
C-Terminally fused affinity Strep-tag II is removed by proteolysis from recombinant human erythropoietin expressed in transgenic tobacco plants. PMID:25504272
Protein structure annotation resources. PMID:25502191
A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif. PMID:25461536
Antifreeze proteins enable plants to survive in freezing conditions. PMID:25431421
Uncertainty in integrative structural modeling. PMID:25173450
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). PMID:25161240
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. PMID:24782522
An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation. PMID:24365473
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
ModBase, a database of annotated comparative protein structure models and associated resources. PMID:24271400
Protein modeling: what happened to the "protein structure gap"? PMID:24010712
Comparative protein structure modeling using Modeller. PMID:18428767
Tags:
Tags
More detailed information about this field from each metasource.
protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:58.650893
structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:58.650893
proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:58.650893
molecular modelling
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:58.650893
Tags
More detailed information about this field from each metasource.
protein folds and structural domains
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:58.650893
structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:58.650893
proteomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:58.650893
molecular modelling
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:58.650893
protein folds and structural domains structure analysis proteomics molecular modelling
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