Bioinformatik-Praktikum II UE 4std

Eine Anwendung aus dem Bereich Proteinstrukturvorhersage

Anrechenbar als Wahlfach in Chemie (419) und Molekulare Biologie (490).

Literatur:

• Moult et.al. "CASP: Round IV"
• Fisher et.al "... automated structure prediction methods"
• Tramantano et.al. "...comparative modelling predictions in CASP4"
• Sippl et.al "..CASP4 Fold Recognition Category"
• Venclovas et.al "Comparison of performance in successive CASP experiments"
• Koretke et.al "Fold recognition from sequence comparisons"

Protein structure prediction links:

Secondary Structure Predictors

PredictProtein
Predator (currently no web-service available)
Cohen's nnpredict
PSIPRED
Solovyev and Salamov's SSP
King and Sternberg's DSC (old version)
PSA from BU
Jpred Helix Start prediction from the Universities of Split and Osijek

(You can extract the secondary structure from a PDB-file with the locally installed program stride)

Threading and fold recognition

PDBblast
Superfamily structural assignment
FUGUE fold recognition
3dpssm
SAM-T02 (HMM-based)
123D, SARF2 and PDP
FFAS03
INBGU
3D JIGSAW
UCLA-DOE Fold Server
LOOPP
PsiPred prediction server
Libellula
ExPASy Molecular Biology Server
SWISS-MODEL automated homology model building tool
Modeller comparative homology modeling of proteins

Comparison and Validation
SARF2 Interactive Structural Superposition
Protein Geometry Web site by Mark Gerstein
EMBL biocomputing 3D modelling unit server page
Dali (Holm & Sander) 3D structure comparison
Biotech Structure Validation suite
WhatIf Web Interface
Procheck (locally installed)