Index of Resources

Protein Structure: Guides, Tutorials, & Primers

Downloadable 3-D protein structure viewers

Structure Prediction & Modeling

2D Structure Predidtion Analysis

Transmembrane Helices

Homology Modelling Servers

Fold recognition methods

3D Structure Analysis

Protein Structure & Information Databases

Specific Protein Information & Databases

Physico-Chemical Analysis of Protein Structures

On-Line Structure Viewing

Database Information Retrieval Servers

• A Guide to [Protein] Structure Prediction at BMM (UK)
• MODULES in Extracellular Proteins at EMBL-Heidelberg (Germany)
• Atlas of Protein Side-Chain Interactions at UCL (UK)
• Atlas of Side-Chain and Main-Chain Hydrogen Bonding at UCL (UK) Protein Loop Classification at BMM (UK)
• Course in Principles of Protein Structure - A Collaborative Virtual Course at Birkbeck College-London (UK)
• Guide to Geometric Aspects of Protein Structure and Function at Duke U (US)
• Sequence to Structure - Secondary Structure Prediction Short Tutorial at U California-Irvine (US)
• Pedro's BioMolecular Research - A Collection of WWW Links to Information and Services useful to Molecular Biologists

RasMol - thanks to Roger Sayle and Glaxo Wellcome for giving it to the World!

GRASP - developed by Anthony Nichols in Honig Lab.

PREPI - developed by Suhail A. Islam at BML (UK)

O and other useful programs - from Uppsala Software Factory.

• Chou-Fassman - Secondary Structure Prediction at BMERC-Boston U (US)
• COILS - Prediction of Coiled Coiled Regions at;
• Coils - ISREC (Switzerland)
• Coils - BCM (US)
• EvalSec - Evaluation of Secondary Structure Prediction Accuracy at EMBL-Heidelberg (Germany)
• DSC - at ICRF
• Garnier-Robson-Osguthorpe - Secondary Structure Prediction at;
• Garnier-Robson-Osguthorpe - BMB-BG U Leeds (UK)
• GDE-Garnier Prediction - IMB-Jena (Germany)
• GOR4 - ABS-NIH (US)
• GOR - U Southhampton (UK)
• PSSP - Protein Secondary Structure Predictor by different methods at BCM
• PREDATOR - Protein Secondary Structure Prediction (& Info) at EMBL-Heidelburg (Germany)
• PHDsec - Secondary Structure Prediction (& (Info) at EMBL-Heidelberg (Germany)
• Predict Protein [Email Server] - Protein Secondary Structure at Iowa State Univ (US)
• Protein Sequence Analysis - 2D Structure Prediction at IBCP (France)
• PSA - Protein Sequence [Structure Prediction] Server at Boston U (US)
• ProtScale - Secondary Structure Properties Prediction (alpha/beta/turn, mutability, flexibility, polarity, hydrophobicity, accessible surface res., etc.) at ExPasy (Switzerland)
• QLSSP - Quadratic Logistic Secondary Structure Prediction at;
• QLSSP (without Homologuous Sequences) - ABS-NIH (US)
• QLSSP (using Homologuous Sequences) - ABS-NIH (US)
• SSCP - Secondary Structural Content Prediction (& Info) at EMBL-Heidelberg (Germany)
• SOPM - Self Optimized Prediction Method and other methods for Secondary Structure Prediction Service at IBCP-CNRS (France)
• SSPRED - Secondary Structure Prediction at EMBL-Heidelberg (Germany)
• ZPRED - MultPredit Secondary Structure of Multiply Aligned Protein Analysis at the Ludwig Institute for Cancer Research (UK)

• DAS - Transmembrane Prediction from a Query Sequence at Biochem D-Stockholm U (Sweden)
• PHDhtm - Predict Transmemebrane Helices (& Info) at EMBL-Heidelberg (Germany)
• PHDtopology - Predict Topology (N-Terminal Orientation) of Transmemebrane Helices at ( & Info) EMBL-Heidelberg (Germany)
• SOSUI - Prediction of Transmembrane Regions at Tokyo U Ag & Techn (Japan)
• TMAP - Analysis of Protein Transmembrane Regions rom multiple sequence alignment at Karolinska Institut.
• TMPRED - Protein Transmembrane Region Prediction at;
• TMPRED - ISREC (Switzerland)
• TMpred - BCM (US)
• TopPred2 - Topology Prediction of Membrane Proteins at Biochem D-Stockholm U (Sweden)
• HMMTOP - new HMM based topology predictor (Hungary)
• TMHMM - another HMM based predictor at CBS Danmark.

• Swiss-Model - Protein Modeling Server at ExPASy (Switzerland)

• 123D Threading - Secondary Structure Prediction (& Info) at;
• GMD-SCAI - SCAI.ALG (Germany)
• 123D at LLNL (US)
• FoReSST - Fold Recognition from Secondary Structure at DCRT-NIH (US)
• PredictProtein - (TOPITS) Fold Recognition by Structure Prediction-Based Threading (& Info) at EMBL-Heidelberg (Germany)
• Protein Fold Recognition Server - Prediction of Structural Folds in Proteins at UCLA/DOE-MBI (US)
• UCLA-DOE Structure Prediction Server - Protein Fold Recognition Analysis at UCLA/DOE-MBI (US)
• THREADER - program for prediction of the protein tertiary structure by recognising the correct fold from a library of alternatives.
• Protein Structure Prediction Centre (US)
• Threading at NCBI (S.H. Bryant)

• Biotech Validation Suite for Protein Structures
• Biotech Validation Suite for Protein Structures at EMBL-Heidelberg (D)
• Biotech Validation Suite for Protein Structures at EBI (UK)
• Biotech Validation Suite for Protein Structures at PDB BNL (USA)
• CLUSTPROT - Determines Spatial Clusters in Proteins based upon Residue Contacts (& Info) at EMBL-Heidelberg (Germany)
• DALI - Structure-to-Structure Comparison using Structures Modeled from PDB and User-Supplied Structure Coordinates at EBI (UK)
• ERRAT - Protein Structure Verification at UCLA-DOE (US)
• PROCHECK - checks the stereochemical quality of a protein structure at UCL (UK)
• PROMOTIF - analyses a protein structure and provides details of the structural motifs at UCL (UK)
• LIGPLOT - plotts protein-ligand interaction.
• SCARF2 - Protein Structure (PDB) Comparison at LEMB (US)
• STRIDE - Protein Secondary Structure Assignment from Atomic Coordinates (& Info) at EMBL-Heidelberg (Germany)
• SAM - Sequence Alignment and Modeling system
• SAS - Sequences Annotated by Structure at UCL (UK)
• Verify3D - 3D Structure Evaluation Service at UCLA-DOE (US)

• BMCD - Biological Macromolecule Crystallization Database at CARB (US)
• BioMagResBank - Database of NMR-derived Protein Structures at BIMAS-NIH (US)
• CATH - Protein Structure Classification at the UCL (UK)
• CATHWheels - Distributions of Protein Folds. Includes a server to generate your own CATHWheels.
• CAMPASS - CAMbridge database of Protein Alignments organised as Structural Superfamilies
• CCDC - Cambridge Structural Database (UK)
• CCP11 - Biosequence & Structural analysis (UK)
• DALI - Comparison of protein structures in 3D at EBI (UK)
• DDBASE - Database of protein structural domains Cambridge (UK)
• DSSP - Definitions of the Secondary Structures of Proteins Database (based upon PDB 3D coordinates) [DSSP Program info] at EMBL-Heidelberg (Germany)
• DbBrowser at UCL (UK)
• Enzyme Structure Database (of enzymes in PDB) UCL (UK)
• ExPaSy ENZYME - Enzyme nomenclature database
• FSSP - Families of Structurally Similar Proteins Database at EBI (UK)
• FTHOM - Protein Domain Homology Analysis (& Information) at ABC (Hungary)
• HOMSTRAD - HOMologous STRucture Alignment Database Cambridge (UK)
• HSSP - Homology-derived Secondary Structure of Proteins Dayabase at EMBL-Heidelberg (Germany)
• Kinemage Library of Protein Structure images via the Protein Science Server (US)
• ModBase database of comparative protein structure models (A.Sali, Rockefeller, US)
• MolMovDB - Database of Macromolecular Movements at Yale U (US)
• NRL_3D - Sequence/Structure Database derived from PDB 3-D Protein Structures at:
• NRL_3D - JHU (US)
• NRL_3D - EMBL-Heidelberg (Germany)
• PDB - Protein Database of 3-D Structures of Biological Macromolecules (Annotated Reference Manual) at;
• PDB - Brookhaven National Laboratory (US)
• PDB at European Bioinformatics Institute (UK)
• PDB Search & Browse Resources:
• PDB-At-A-Glance - Hierarchal Glance at PDB Entries at NIH (US)
• PDB-3DBBrowser at EBI (UK)
• PDB-Select Database - is a Subset of the Structures of PDB entries containing (Non)-Homologous Sequences at EMBL-Heidelberg (Germany)
• PDBFINDER - An abbreviated database of PDB, DSSP, and HSSP Entries at EMBL-Heidelberg (Germany)
• PDBREPORT - database of raports describing structural problems in PDB entries at UCL (UK)
• PDBsum - Summaries and structural analyses of PDB files at UCL (UK)
• Picornavirus 3D Protein Structures at the IAH-Picornavirus Home Page (UK)
• RELIBase - object-oriented database for structural data about receptor/ligand complexes EBI (UK)
• SCOP - Structural Classification of Proteins Database at the U Cambridge (UK)
• TOPS - atlas of topology cartoons at EBI (UK)

• G protein-coupled receptors
• 7TM receptor modelling at York (UK)
• GPCR information system at EMBL, Heidelberg.
• GPCR database WWW at Harvard.
• GPCR database at NIH, Bethesda
• GRAP mutant database at Tromso
• Olfactory Receptor Database at Yale
• DbBrowser at UCL (UK)
• Protein kinases
• The Protein Kinase Resource (USA)

Physico-Chemical Analysis of Protein Structures

• ASC - Analytic Surface Calculation of PDB Protein Structures at EMBL-Heidelberg (Germany)
• PHDacc - Protein Structure Solvent Accessibility at EMBL-Heidelberg (Germany)
• PROVE - Protein Volume Evaluator at UCMB (Belgium)

• QuikPDB - Java Interactive Sequence-Structure Viewer at SDSC (US)
• WebMol - Java PDB Viewer at EMBL-Heidelberg (Germany)

• ENTREZ MMDB - Molecular Modeling Database Search (& MMDB FAQ) at NCBI (US)
• Molecules-R-US - PDB Text & Image Retreival Server at NIH (US)
• MOOSE - Macomolecular Object Oriented Search Engine for the PDB Entries at SDSC (US)
• OBSTRUCT - Search for PDB Structures based on Crystal Resolution & Sequence Identity (& Info) at EMBL-Heidelberg (Germany)
• SRSWWW - Network Browser for Databanks in Molecular Biology at EMBL-Heidelberg (Germany)

Compilation done by Pawel Herzyk at York Structural Biology Laboratory.