3-D Structure Prediction
Bioinformatics & Genomics
3-D Structure Prediction
Protein Data Bank (PDB)
Searches of PDB
Secondary Structure Prediction & Assignment
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[EMBL] This page provides information and services for protein 3D modeling.
[CBS] Predicts protein structure using comparative (homology) modelling.
[University of California, Santa Cruz] “DINAMO is an interactive protein model building tool. It allows the user to build simple, three-dimensional models of proteins based on their sequence similarity or predicted fold similarity to proteins whose
structures have been solved experimentally.”
A Guide to Structure Prediction
[Imperial Cancer Research Fund] A guide with links, giving a generalistic approach to prediction of protein structures.
Indiana University Molecular Structure Center
[Indiana University] X-ray crystallography educational resource. The Indiana University Molecular Structure Center is a laboratory specializes in the structural determination of small
[Rockefeller University] Database of comparative protein structure models.
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.
Protein Structure Prediction Center and CASP
[Lawrence Livermore National Laboratory] “Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. In addition to the support of the CASP meetings our goal is to promote an objective evaluation of prediction methods on a continuing basis.” CASP stands for Critical Assessment of techniques for protein Structure Prediction.
Protein Tertiary Structure Tools
[ExPASy] An annotated list of links to tools that provide 3D protein folding and modelling.
PSA: Protein Sequence Analysis Server
[BMERC] Analyzes amino acid sequences to predict secondary structures and folding classes.
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[ExPASy] An automated comparitive protein modelling server.
[Protein Bioinformatics Group, Univ. of Warwick] This program predicts protein tertiary structure by recognizing the correct fold from a library of selections.
[Samuel Lunenfeld Research Institute] TRAjectory Directed Ensemble Sampling is a novel approach to the protein folding problem that employs novel entities known as “trajectory graphs” to guide a growing random walk amino acid polymer, and to construct all-atom models of proteins of arbitrary sequence.
UCLA/DOE Fold Server
[UCLA-DOE] Motif-Based Fold Assignment method combines the
functional information contained in the SwissProt keyword annotation with Prosite
motif database to improve the performance of any conventional
sequence/structure based prediction.
UCLA-DOE Structure Prediction Server
[UCLA] Provides protein fold recognition, sequence analysis, and validation. Output data is formatted in HTML.
[CMBI] This protein structure analysis program can be used for molecular graphics and structure verification.