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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