SurpResi 201108 – Protein Active Site Prediction based on Central Distances of Amino Acids

SurpResi 201108

:: DESCRIPTION

SurpResi is a web-accessible tool for finding binding sites in proteins. The method is based on the probabilitic analysis of global radial distributions of atoms.

::DEVELOPER

Marek Kochańczyk

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

SurpResi

:: MORE INFORMATION

Citation

Kochańczyk, M. (2011)
Prediction of functionally important residues in globular proteins from unusual central distances of amino acids,
BMC Struct. Biol. 11:34 doi:10.1186/1472-6807-11-34.

CAPE – Test Convergent and Parallel Evolution at the Amino Acid sequence level

CAPE

:: DESCRIPTION

Converge (Cape : Convergent and Parallel Evolution at the Amino Acid Sequence Level) was designed to test convergent and parallel evolution at the amino acid sequence level. It computes the probabilities that the observed convergent and parallel substitutions are attributable to random chance.

::DEVELOPER

Jianzhi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
C Compiler

:: DOWNLOAD

Converge

:: MORE INFORMATION

Citation:

Zhang J. and S. Kumar (1997)
Detection of convergent and parallel evolution at the amino acid sequence level.
Mol. Biol. Evol. 14:527-536.

ForCon 1.0 – Conversion of Nucleic Acid & Amino Acid Sequence Alignments

ForCon 1.0

:: DESCRIPTION

ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically.

::DEVELOPER

Jeroen Raes

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

ForCon

:: MORE INFORMATION

Citation

Raes, J. and Van de Peer,Y. (1999)
ForCon : a software tool for the conversion of sequence alignments.
EMBnet.news 6(1).

MODELESTIMATOR 1.1 – Estimate Amino Acid Replacement Rates

MODELESTIMATOR 1.1

:: DESCRIPTION

MODELESTIMATOR estimates amino acid replacement rates from an input of aligned sequences.

::DEVELOPER

Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ windows/MacOsX
Perl

:: DOWNLOAD

MODELESTIMATOR Source Code

:: MORE INFORMATION

Citation:

Lars Arvestad, Efficient methods for estimating amino acid replacement rates, 2006, J Mol Evol, 62(6):663–673.