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PconsC - PconsCPconsC Jan 28th, 2013 Motivation Recently, several new contact prediction methods have been published. They use large sets of multiple aligned …
http://c.pcons.net/
PconsC Jan 28th, 2013 Motivation Recently, several new contact prediction methods have been published. They use large sets of multiple aligned …
http://c.pcons.net/
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PconsC - PconsC | c.pcons.net Reviews
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PconsC Jan 28th, 2013 Motivation Recently, several new contact prediction methods have been published. They use large sets of multiple aligned …
c.pcons.net
Download - PconsC
http://c.pcons.net/download.html
Combination of direct information methods and alignments improves contact prediction. The newest version of PconsC can be retrived from GitHub repository:. Git:/ github.com/mskwark/pconsc.git. Snapshot of PconsC reported in the paper, can be downloaded here. The stable version, that should be used for production use (if desired), can be downloaded here.
Data sets - PconsC
http://c.pcons.net/datasets.html
Combination of direct information methods and alignments improves contact prediction. PconsC has been benchmarked on a set of 150 small-sized proteins (. That have been used in the development of PSICOV. This choice was made in order to allow direct comparison between PconsC and other, published contact prediction methods. The method development of PconsC has been aided by a set of 44 proteins (. Some of the proteins in the. May be homolgous, but the set was kept intact, for the sake of comparability.
Raw data - PconsC
http://c.pcons.net/rawdata.html
Combination of direct information methods and alignments improves contact prediction. The data used to optimize and benchmark PconsC, in the form it was presented in the paper can be downloaded as snapshot ZIP archives: training set. 192 MB) and testing set.
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OPENSEQ.org - GREMLIN FAQ
http://www.openseq.org/gremlin_faq.php
Please contact us if you notice any strange outputs. What is Coevolution, Covariance and Correlated Mutations? For protein coding genes, when a residue mutates a compensatory mutation follows. These mutations are captured in our DNA and in the DNA of all living organisms. By analyzing a MSA (multiple sequence alignment) of homolgous protein sequences, we can measure coupling of any given residue pairs. For proteins with deep alignments, the strength of the co-evolution parameters after correcting for ent...
Software
http://bioinfo.se/software
Protein evolution. Protein structure predictions. Bioinformatics. Our ambition is to develop better methods for prediction of protein structure and function. The most successful methods are provided as web-based servers. Web-services developed through EMBRACE. A program for homology modelling. A program for Hidden Markov Model-based homology scoring. Ultra rapid, accurate model quality assessment for protein structure prediction. A predictor of protein quality. Membrane Protein Topology Prediction Methods.
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PconsC - PconsC
Combination of direct information methods and alignments improves contact prediction. Recently, several new contact prediction methods have been published. They use large sets of multiple aligned sequences and assume that correlations between columns in these alignments can be the results of indirect interaction. We demonstrate that combining predictions from two prediction methods, PSICOV. And two alignment methods, HHblits. The source code for PconsC is freely available at http:/ c.pcons.net/.
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