Structure Prediction & Modeling

Physico-Chemical Analysis of Protein Structures

Protein Structure & Information Databases

Structure Visualization

Protein Structure: Guides, Tutorials & Primers

Protein Structure: Projects & Initiatives

Structure Prediction & Modeling 2D & 3D Structure Prediction Analyses 123D Threading - Secondary Structure Prediction - LECB (US) 3D-PSSM - Protein Fold Recognition Using 1/3D Sequence Profiles with 2D Info - BMM (UK) AGADIR - Protein Helical Content Predictor - EMBL-Heidelberg (Germany) CE - 3D Structure Comparison & Alignment - SDSC (US) CLUSTPROT - Determines Spatial Clusters in Proteins based upon Residue Contacts - EMBL-Heidelberg (Germany) CODA - Predicting Loops in Protein Structure - U Cambridge (UK) COILS - Prediction of Coiled Coiled Regions Coils - IBCP (France) Coils - ISREC (Switzerland) Coils - BCM (US) COMPARER ON-LINE - Protein Structure Superposition Comparison - U Cambridge (UK) DALI - Structure-to-Structure Comparison using Structures Modeled from PDB and User-Supplied Structure Coordinates - EBI (UK) DOMAINS - Protein Domains Analysis Server - BMM (UK) DPM - Double Prediction Method for Secondary Structure - IBCP (France) DSC - Secondary Structure Prediction - IBCP (France) FoReSST - Fold Recognition from Secondary Structure - ABS/NIH (US) FUGUE - Structure Profile Library Search against HOMSTRAD DB - U Cambridge (UK) Garnier - Osguthorpe - Robson - Secondary Structure Prediction GARNIER (GOR1) - IBCP (France) GIBRAT (GOR3) - IBCP (France) GOR IV - IBCP (France) GDE-Garnier Prediction - IMB-Jena (Germany) Garnier-Osguthorpe-Robson - BMB-BG U Leeds (UK) GOR - U Southhampton (UK) GOR IV - ABS-NIH (US) GRASS - Graphical Representation and Analysis of Structure Server - Columbia U (US) HNN - Hierarchical Neural Net Secondary Structure Prediction - IBCP (France) HTH - Helix-Turn-Helix Motif Prediction - IBCP (France) JOY - Protein Structure & Alignment Analysis - U Cambridge (UK) MLRC - Secondary Structure Prediction - IBCP (France) nnPredict - Secondary Structure Prediction nnPredict - UCSF (US) nnPredict - BCM (US) NNSSP-PSSP - Nearest-Neighbor 2D Structure Prediction NNSSP-PSSP (1) - BCM (US) NNSSP-PSSP (2) - BCM (US) Paircoil - Prediction of Coiled Coil Regions Paircoil - MIT (US) Paircoil - BCM (US) PHD - IBCP (France) PREDATOR - Secondary Structure Prediction PREDATOR - IBCP (France) PREDATOR - EMBL-Heidelburg (Germany) Predict Protein - Secondary Structure Prediction PredictProtein - EMBL-Heidelberg (Germany) PredictProtein - Columbia (US) PROF - Secondary Structure Prediction - BMM (UK) Protein Fold Recognition Server - Prediction of Structural Folds in Proteins - UCLA/DOE-MBI (US) ProtScale - Secondary Structure Properties Prediction - ExPasy (Switzerland) PSA - Protein Sequence [Structure Prediction] Server - Boston U (US) QLSSP - Quadratic Logistic Secondary Structure Prediction QLSSP (w/o Homologuous Sequences) - ABS-NIH (US) QLSSP (w/ Homologuous Sequences) - ABS-NIH (US) SAWTED - Structure Alignment With Text Description - BMM (UK) SIPMA96 - HOMOLOGUE Secondary Structure Prediction - IBCP (France) SOPM - Self Optimized Prediction Method for Secondary Structure Prediction Service - IBCP (France) SOPMA - SOPM Secondary Structure Prediction - IBCP (France) SSCP - Secondary Structure Prediction SSCP-AA - Prediction from Amino Acid Composition - EMBL-Heidelberg (Germany) SSCP-Seq - Prediction from Protein Sequence - EMBL-Heidelberg (Germany) SSP-PSSP - Segment-Oriented 2D Structure Prediction SSP-PSSP (1) - BCM (US) SSP-PSSP (2) - BCM (US) STRIDE - Protein Secondary Structure Assignment from Atomic Coordinates - EMBL-Heidelberg (Germany) Swiss-Model - Protein Modeling Server - ExPASy (Switzerland) TargId - Protein Structure Prediction - GMD-SCAI (Germany) UCLA-DOE Structure Prediction Server - Protein Fold Recognition Analysis - UCLA/DOE-MBI (US) VAST - Structure-Structure Similarity Search - NCBI (US) ZPRED - MultPredit Secondary Structure of Multiply Aligned Proteins - Ludwig Inst for Cancer Res (UK) 3D Protein Structure Comparison & Analysis BVSPS - Biotech Validation Suite for Protein Structures BVSPS - EMBL-Heidelberg (Germany) BVSPS - EMBL-EBI (UK) ERRAT - Protein Structure Verification - UCLA-DOE (US) MolSurfer - Navigating Protein-Protein Interfaces - EMBL-Heidelberg (Germany) SCARF2 - Protein Structure Comparison - LEMB (US) SwissModel - Automated Protein Modeling - ExPasy (Switzerland) Verify3D - 3D Structure Evaluation Service - UCLA-DOE (US) Physico-Chemical Analysis of Protein Structures ASC - Analytic Surface Calculation of PDB Protein Structures - EMBL-Heidelberg (Germany) PHDacc - Protein Structure Solvent Accessibility - EMBL-Heidelberg (Germany) Protein Structure & Information Databases 3D-ALI - Protein Structural-Sequence Information Library - EMBL-Heidelberg (Germany) BioMagResBank - Database of NMR-derived Protein Structures - BIMAS-NIH (US) BMCD - Biological Macromolecule Crystallization Database - CARB (US) CAMPASS - CAMbridge DB of Protein Alignments organized as Structural Superfamilies - U Cambridge (UK) CATH - Protein Structure Classification at the - U College London (UK) Culled PDB - Unique/Representative Proteins in the PDB - Fox Chase Cancer Center (US) DIP - Database of Interacting Proteins - UCLA-DOE (US) DSMP - Database of Structural Motifs in Proteins - CDFD (India) DSSP - Definitions of the Secondary Structures of Proteins Database - EMBL-Heidelberg (Germany) ENTREZ Structure - Biomolecule 3D Structure Search - NCBI (US) Enzyme Structure Database - UCL (UK) FSSP - Families of Structurally Similar Proteins Database - EBI (UK) HAD - Heavy Atom Databank - BMM (UK) HIC-Up - Hetero-Compound Information Centre-Uppsala - Uppsala U (Sweden) HOMSTRAD Search & Browse Resources HOMSTRAD Keyword Search - U Cambridge (UK) IMPOSE - Search HOMSTRAD & CAMPASS DB's for Proteins with Similar 3-D Motifs - U Cambridge (UK) HOMSTRAD - Homologous Structure Alignment Database - U Cambridge (UK) HOMSTRAD/PLUS - HOMSTRAD DB with Pfam/HOMS - U Cambridge (UK) Kinemage Library - Protein Science (US) LOOP - Protein Loop Classification Database - BMM (UK) MMDB - ENTREZ Molecular Modeling Database - NCBI (US) MolMovDB - Database of Macromolecular Movements - Yale U (US) MSD - Macromolecular Structures Database - BioMedNet (US) NRL_3D Search & Browse Resources NRL_3D Text/Entry Search - NBRF (US) NRL_3D Sequence Gapped-BLAST Similarity Search - NBRF (US) NRL_3D - Sequence-Structure Database - NBRF (US) PDB - Protein Database of 3-D Structures of Biological Macromolecules PDB - U Federal de Mina Gerais (Brazil) PDB - U Osaka (Japan) PDB - Nat U Singapore (Singapore) PDB - CCDC (UK) PDB - San Diego Supercomputer Center (US) PDB - Rutgers (US) PDB - NIST (US) PDB Search & Browse Resources PDBLite - ANGIS (Australia) PDB-Select Database - is a Subset of the Structures of PDB entries containing (Non)-Homologous Sequences - EMBL-Heidelberg (Germany) PDBFINDER - An abbreviated database of PDB, DSSP, and HSSP Entries - EMBL-Heidelberg (Germany) OCA - PDB Search Tool - Weizmann Institute (Israel) PDBLite - Weizmann Institute (Israel) PDB Search (DBGET) - GenomeNet (Japan) PDBLite - CCDC (UK) MOOSE - Macromolecular Object Oriented Search Engine for the PDB Entries - SDSC (US) SearchFields - ADvanced PDB Search - RCSB (US) SearchLite - Simple Keyword PDB Search - RCSB (US) PDB-At-A-Glance - Hierarchal Glance at PDB Entries - NIH (US) PDBLite - Boston U (US) Picornavirus 3D Protein Structures - IAH-Picornavirus Home Page (UK) PIR - Protein Information Resource Database - NBRF (US) PIR Search & Browse Resources PIR Gapped-BLAST Similarity Search - NBRF (US) PIR Text/Entry Search - NBRF (US) PRESAGE - Database and Search Tools for Structural Genomics - Stanford U (US) Protein Loop Classification - BMM (UK) SCOP - Structural Classification of Proteins Database SCOP - Walter & Eliza Hall Inst (Australia) SCOP - ANGIS (Australia) SCOP - CDFD (India) SCOP - Maduri Kamaraj U (India) SCOP - Weizmann Institute (Israel) SCOP - BERI (Japan) SCOP - Inst Protein Research (Russia) SCOP - Nat U Singapore (Singapore) SCOP - Nat Tsing Hua U (Taiwan) SCOP - U Cambridge (UK) SCOP - U California-Berkeley (US) SLoop - Database of Super Secondary Fragments - U Cambridge (UK) SPIN-PP - Surface Properties of INterfaces - Protein Protein Interfaces - Columbia U (US) TOPS - Protein Topology - EBI (UK) Structure Visualization On-Line Viewing (JAVA) Protein Explorer - Protein Structure Explore Tool - U Massachusetts (US) QuikPDB - Java Interactive Sequence-Structure Viewer - SDSC (US) WebMol - Java PDB Viewer - EMBL-Heidelberg (Germany) Browser Plug-In Applications (for On/Off-Line Viewing) Chime (Chemscape) - Visualization Tool - MDL (US) Cn3D - 3-D Structure Viewer - NCBI (US) MAGE - Kinemage Image Viewing - Duke U (US) RasMol - Molecular Visualization - U Massachusetts (US) Protein Structure: Guides, Tutorials & Primers A Guide to [Protein] Structure Prediction - BMM (UK) Atlas of Protein Side-Chain Interactions - UCL (UK) Atlas of Side-Chain and Main-Chain Hydrogen Bonding - UCL (UK) MODULES in Extracellular Proteins - EMBL-Heidelberg (Germany) Molecules-R-US - PDB Text & Image Retreival Server - NIH (US) Principles of Protein Structure Using the Iternet - Birkbeck College-London (UK) Quick Guide to Finding Sequence Homologues - U Cambridge (UK) Protein Structure: Projects & Initiatives ISGB - NJCST-Initiative in Structural Genomics & Bioinformatics - U Rutgers (US) JCSG - Joint Center for Structural Genomics (US) PPA - Proteome of Pyrobaculum Aerophilum - U California-LLNL (US) PSI - Structural Genomics Initiative (US) S2F - Structure 2 Function - NIST (US) SGR - Structural Genomics Research - Argonne Nat Lab (US) SGRC - Structural Genomics Research Initiative (US) Last modified 13 March 2003 by Christopher M. Smith at CMSMBR - SDSC Copyright © 1996-2001 Christopher M. Smith & The Regents of the University of California