Protein Structure Prediction Links
[Secondary Structure] [Fold Prediction] [Other Methods] [Miscellany]

Secondary Structure Prediction
  • BCM Launcher - excellent secondary structure prediction launcher
  • Consensus - combines 5 methods, including PHD (IBCP)
  • DAS - Dense Alignment Surface method for transmembrane helix prediction (Stockholm Uni.)
  • DSC - Discrimination of protein Secondary structure Class, with manual (King & Sternberg, ICRF)
  • GOR IV - method derived from information theory (Garnier, Osguthorpe & Robson, ABS)
  • GOR - with enhanced interface (Southampton Uni.)
  • K2d - uses Kohonen net to estimate structure from UV CD (Andrade et al.)
  • NNPREDICT - 2-layer feed-forward neural net (Cohen Group)
  • PEPPLOT - secondary structure and hydrophobicity plots (Genetics Computer Group)
  • PHD - Profile neural network prediction from HeiDelberg (EMBL)
  • PREDATOR - single sequence or pairwise local alignments (Argos group)
  • PSSP (SSP/NNSSP) - segment-oriented or nearest-neighbour prediction (BCM)
  • QL - Quadratic Logistic with/without homologues (ABS)
  • SIMPA96 - secondary structure prediction (EMBL)
  • SOPM (and SOPMA) - Self Optimized Prediction Method (from Alignment) (IBCP)
  • SOSUI - secondary structure prediction, membrane proteins (GenomeNet, Japan)
  • SSCP - Secondary Structural Content Prediction (Eisenhaber, EMBL)
  • SSPRED - neural network method (Mehta et al., EMBL)
  • Zpred - method with multiple alignements (Zvelebil et al., Ludwig)

    • Fold Prediction
  • 123D (PROTAL, GMD)
  • PSA - Protein Seqeunce Analysis, both structure and folding class (BMERC)
  • RDP - threading by Recursive Dynamic Programming (GMD)
  • THREADER - fold recognition (David Jones, Warwick University)
  • UCLA-DOE - fold-recognition server (UCLA)

    • Other Prediction Methods
  • BrainMaker - analysis of transmembrane-spanning helices (Dombi, Wayne State Uni.)
  • COILS - prediction of coiled-coil regions (ISREC)
  • NetOglyc v1.1 - neural net prediction of O-glycosylation sites (CBS)
  • Paircoil - prediction of coiled-coil regions (MIT)
  • PREDBB documentation - beta-strand pair prediction (IRBM course)
  • PSORT - expert system predicting sorting signals and localisation sites (NIBB, Japan)
  • SignalP v1.1 - neural net prediction of signal peptide cleavage sites (CBS)
  • TMAP - prediction of protein transmembrane segments (EMBL)
  • TMpred - transmembrane regions and orientation (ISREC)

    • Miscellany
  • CASP - Critical Assessment of techniques for protein Structure Prediction (PSPC)
  • FEBS Course - Frontiers of Protein Structure Prediction 1995/1997 (IRBM)
  • Overview about computer-based methods and tools for secondary structure prediction (Ekard Burger, Heidelberg)
  • ProStar - the Protein Potential Site (CARB)
  • PROTEIN - protein structure analysis and prediction project (SCAI, GMD)
  • PSPC - Protein Structure Prediction Center (Lawrence Livermore Nat. Lab.)
  • Qian & Sejnowski Data - data set for seminal neural net paper (JMB 202, 1988)
  • Structure Prediction Guide (Robert Russell, ICRF)