Protein structure prediction

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Secondary and tertiary protein structure prediction. Information about the secondary and tertiary structure of a protein sequence can greatly assist biologists in the generation and testing of hypotheses, as well as design of experiments. The PROTINFO server enables users to submit a protein sequence and request a prediction of the three-dimensional (tertiary) structure based on comparative modeling, fold generation and de novo methods developed by the authors. In addition, users can submit NMR chemical shift data and request protein secondary structure assignment that is based on using neural networks to combine the chemical shifts with secondary structure predictions.<pubmed argument="PROTINFO">12824311</pubmed>

GeneSilico - Fold Prediction Metaserver
Aligns the target sequence to sequences of proteins with known structures, identified by protein fold-recognition (FR) methods. The Pcons consensus server will evaluate to which extent the FR alignments agree with each other and if a particular fold can b
Protein structure prediction meta-server. Gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection.<pubmed argument="GeneSilico - Fold Prediction Metaserver">12824313</pubmed>

The DSSP software and database The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries ...

Protein Structure Prediction Center
Critical Assessment of Techniques for Protein Structure Prediction. Community Wide Experiments on the critical assessment of techniques for protein structure prediction. Advances the methods of identifying protein structure from sequence.

CUPSAT - Cologne University Protein Stability Analysis Tool
CUPSAT predicts changes in protein stability upon point mutations, using amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site, solvent accessibility and secondary structure specificity.

An Energy-Based Protein Structure Prediction Server
Developed by IIT Delhi, Bhageerath accepts amino acid sequence and secondary structure information to predict 100 candidate structures for the native proteins.

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