CCMpred 0.3.2 – Prediction of Protein Residue-residue Contacts from Correlated Mutations

CCMpred 0.3.2

:: DESCRIPTION

CCMpred is a C implementation of a Markov Random Field pseudo-likelihood maximization for learning protein residue-residue contacts

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
:: DOWNLOAD

 CCMpred

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jul 26. pii: btu500.
CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations.
Seemayer S1, Gruber M1, Söding J

ProACT 2 – Analysis of Protein Accessibilities, Cavities and Contacts

ProACT 2

:: DESCRIPTION

ProACT is a widely used software for the anlysis of protein accessibilities, cavities and contacts and structural/buried water molecules.

::DEVELOPER

Mark A. Williams

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ProACT

:: MORE INFORMATION

Citation

Tjelvar S.G. Olsson, Antony M.E. Churchill, William R. Pitt, John E. Ladbury & Mark A. Williams (2012).
ProACT2 – Analysis of solvent accessibility, cavities and contacts in proteins and their complexes.
Submitted

TMHcon 20101215 – predict Contacts for Transmembrane Proteins

TMHcon 20101215

:: DESCRIPTION

TMHcon is a software to predict helix-helix contacts specifically within the transmembrane parts of membrane proteins. It includes predictions by two different neural networks, one developed for helix-helix contacts on all transmembrane helix pairs and one specifically tailored for the prediction of helix-helix contacts lying on non-neighboring transmembrane helices.

::DEVELOPER

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 TMHcon

:: MORE INFORMATION

Citation

Proteins. 2009 Mar;74(4):857-71. doi: 10.1002/prot.22194.
Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks.
Fuchs A1, Kirschner A, Frishman D.