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Databases/Tools
NAR database/Web Server and OBRC
The PredictProtein server
Predict protein structure and function based on protein sequence.
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AggreProt: a web server for predicting and engineering aggregation prone regions in proteins.
Nucleic Acids Res. 2024 Jul 05;52(W1)
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DOMAC -- a hybrid protein domain prediction server
An accurate protein domain prediction server.
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CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds.
Nucleic Acids Res. 2024 Jul 05;52(W1)
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The MPI Bioinformatics Toolkit for protein sequence analysis
Conduct protein sequence and structure analysis using a suite of software tools.
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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families.
Nucleic Acids Res. 2024 Jul 05;52(W1)
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Protein structure prediction servers at University College London
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PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks.
Nucleic Acids Res. 2023 Jul 05;51(W1)
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EVA -- evaluation of protein structure prediction servers
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InterPro in 2022.
Nucleic Acids Res. 2023 Jan 06;51(D1)
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Integrated databanks access and sequence/structure analysis services at the PBIL
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TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures.
Nucleic Acids Res. 2023 Jan 06;51(D1)
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The Yeast Resource Center Public Data Repository
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HProteome-BSite: predicted binding sites and ligands in human 3D proteome.
Nucleic Acids Res. 2023 Jan 06;51(D1)
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PROSPECT-PSPP -- An automatic computational pipeline for protein structure prediction
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DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction.
Nucleic Acids Res. 2022 Jul 05;50(W1)
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PROTEUS2 -- a web server for comprehensive protein structure prediction and structure-based annotation
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LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.
Nucleic Acids Res. 2022 Jul 05;50(W1)
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PROTINFO -- new algorithms for enhanced protein structure predictions
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dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.
Nucleic Acids Res. 2022 Jan 07;50(D1)
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Pcons.net -- protein structure prediction meta server
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DeepRefiner: high-accuracy protein structure refinement by deep network calibration.
Nucleic Acids Res. 2021 Jul 02;49(W1)
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Robetta Server -- Protein structure prediction and analysis
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AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.
Nucleic Acids Res. 2020 Jul 02;48(W1)
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SAM-T08 -- HMM-based Protein Structure Prediction
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LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.
Nucleic Acids Res. 2019 Jul 02;47(W1)
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(PS)2 -- Protein Structure Prediction Server
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Nucleic Acids Res. 2018 Jul 02;46(W1)
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GeneSilico protein structure prediction meta-server
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GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.
Nucleic Acids Res. 2017 Jul 03;45(W1)
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META-PP -- single interface to crucial prediction servers
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(PS)2: protein structure prediction server version 3.0.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes
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RBO Aleph: leveraging novel information sources for protein structure prediction.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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Decoys 'R' Us
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I-TASSER server: new development for protein structure and function predictions.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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VADAR -- a web server for quantitative evaluation of protein structure quality
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IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
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BPROMPT -- a consensus server for membrane protein prediction
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BCM Search Launcher
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NCI -- a server to identify non-canonical interactions in protein structures
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BOMP -- A Program to Predict Integral xdf-barrel Outer Membrane Proteins Encoded within Genomes of Gram-negative Bacteria
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DSSPcont -- continuous secondary structure assignments for proteins
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ESPript/ENDscript -- extracting and rendering sequence and 3D information from atomic structures of proteins
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EVAcon -- a protein contact prediction evaluation service
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GTOP -- Genomes to Protein structures and functions database
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Geno3D -- Protein Modeling Tool
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GlobPlot -- exploring protein sequences for globularity and disorder
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I-TASSER: Protein Structure & Function Predictions
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Localizome -- a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
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PEP-FOLD -- De Novo Peptide Structure Prediction
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PONGO -- a web server for multiple predictions of all-alpha transmembrane proteins
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PRED-TMBB -- A Web Server for Predicting the Topology of xdf-barrel Outer Membrane Proteins
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PatchDock and SymmDock -- servers for rigid and symmetric docking
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ProTarget -- automatic prediction of protein structure novelty
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QMEAN -- Server for Model Quality Estimation
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SAHG -- Structural Atlas of the Human Genome
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SCRATCH -- a protein structure and structural feature prediction server
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SPROUTS -- Structural Prediction for Protein Folding Utility System
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SWISS-MODEL -- an automated protein homology-modeling server
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Scooby-domain -- prediction of globular domains in protein sequence
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TRAMPLE -- the transmembrane protein labeling environment
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The HHpred interactive server for protein homology detection and structure prediction
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The Jpred 3 secondary structure prediction server
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Tools for comparative protein structure modeling and analysis
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wwLigCSRre -- Ligand-based Screening server
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Find More Resources from PubMed Articles
GalaxyWEB server for
protein structure prediction
and refinement.
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Journal:
Nucleic Acids Res. 2012 Jul;40(Web Server issue)
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GSAFold: a new application of GSA to
protein structure prediction
.
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Journal:
Proteins. 2012 Aug;80(9)
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KoBaMIN: a knowledge-based minimization web server for protein structure refinement.
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Journal:
Nucleic Acids Res. 2012 Jul;40(Web Server issue)
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Network properties of protein-decoy structures.
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Journal:
J Biomol Struct Dyn. 2012;29(6)
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The MULTICOM toolbox for
protein structure prediction
.
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Journal:
BMC Bioinformatics. 2012 Apr 30;13
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β-sheet topology prediction with high precision and recall for β and mixed α/β proteins.
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PLoS One. 2012;7(3)
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Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.
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Journal:
Methods Mol Biol. 2012;857
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Uncluttered Single-Image Visualization of Vascular Structures Using GPU and Integer Programming.
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Journal:
IEEE Trans Vis Comput Graph. 2013 Jan;19(1)
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Measuring the distance between multiple sequence alignments.
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Journal:
Bioinformatics. 2012 Feb 15;28(4)
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Prediction of protein tertiary structures using MUFOLD.
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Journal:
Methods Mol Biol. 2012;815
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