ABS-Scan – Webserver for Insilico Binding site Alanine Scanning Mutagenesis

ABS-Scan

:: DESCRIPTION

ABS-Scan performs alanaine scanning mutagenesis for a given protein-ligand complex.

::DEVELOPER

Chandra Lab, Dept. of Biochemistry.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex.
Anand P, Nagarajan D, Mukherjee S, Chandra N.
Version 2. F1000Res. 2014 Sep 9 [revised 2014 Dec 1];3:214. doi: 10.12688/f1000research.5165.2. eCollection 2014.

DMAN 2.6 – Differential Scanning Fluorimetry Melting Data analysis

DMAN 2.6

:: DESCRIPTION

DMAN is a program to analyse protein thermal denaturation data obtained by multi-well differential scanning fluorimetry. Experimental repetition schemes on multi-well plates can be defined using an ASCII file or through a graphical user interface (GUI).

::DEVELOPER

Hofmann Laboratory, Eskitis Institute

:: SCREENSHOTS

DMAN

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 DMAN

 :: MORE INFORMATION

Citation

Wang, C.K., Weeratunga, S.K., Pacheco, C.M., Hofmann, A. (2012)
DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments.
Bioinformatics 28, 439-440.

SCANPS 2.3.11 – Protein Sequence Scanning Package

SCANPS 2.3.11

:: DESCRIPTION

SCANPS is a sequence database searching program that implements a range of sensitive algorithms for searching protein sequence databases.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SCANPS

:: MORE INFORMATION

Citation:

Thomas P. Walsh1, Caleb Webber, Stephen Searle, Shane S. Sturrock and Geoffrey J. Barton
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
Nucl. Acids Res. (2008) 36 (suppl 2): W25-W29.

omega-statistic – Scanning for Selection in Genomics Regions

omega-statistic

:: DESCRIPTION

The omega-statistic can be used for scanning for selection in genomics regions.  It is based on the signature of a recent selective sweep: the Linkage-Disequilibrium on each side of the beneficial allele is high but low across it.

::DEVELOPER

Pavlos Pavlidis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 omega-statistic

:: MORE INFORMATION

Citation

Genetics. 2004 Jul;167(3):1513-24.
Linkage disequilibrium as a signature of selective sweeps.
Kim Y, Nielsen R.

MotifScan – DNA Motif Scanning

MotifScan

:: DESCRIPTION

MotifScan is a non-parametric DNA motif scanning algorithm.

::DEVELOPER

The Batzoglou Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006;34(20):5730-9.
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.
Naughton BT, Fratkin E, Batzoglou S, Brutlag DL.

ps_scan 1.79 – PROSITE scanning program

ps_scan 1.79

:: DESCRIPTION

ps_scan (ScanProsite tool) is a perl program used to scan one or several patterns, rules and/or profiles from PROSITE against one or several protein sequnces in Swiss-Prot or FASTA format. It requires two compiled external programs from the PFTOOLS package : “pfscan” used to scan a sequence against a profile library and “psa2msa” which is necessary for the “-o msa” output format only.

::DEVELOPER

ExPASy , Swiss Institute of Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Perl

:: DOWNLOAD

 ps_scan

:: MORE INFORMATION

Citation

Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch.
ScanProsite: a reference implementation of a PROSITE scanning tool.
Applied Bioinformatics 2002:1(2) 107-108.

mpiCUDA-BLASTP 1.0 – Accelerate BLASTP for Scanning Protein Sequence databases on GPU clusters

mpiCUDA-BLASTP 1.0

:: DESCRIPTION

mpiCUDA-BLASTP is designed to accelerate BLASTP for scanning protein sequence databases on GPU clusters, programmed using CUDA, MPI, and OpenMP programming models.

::DEVELOPER

Liu Weiguo (liuweiguo@ntu.edu.sg).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mpiCUDA-BLASTP

:: MORE INFORMATION