bSiteFinder – Protein-binding Sites Prediction Server

bSiteFinder

:: DESCRIPTION

bSiteFinder is a web server for indentifying protein-binding sites.

::DEVELOPER

bSiteFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.
Gao J, Zhang Q, Liu M, Zhu L, Wu D, Cao Z, Zhu R.
J Cheminform. 2016 Jul 11;8:38. doi: 10.1186/s13321-016-0149-z.

ChIPseqR 1.26.0 – Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR 1.26.0

:: DESCRIPTION

ChIPseqR is an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments.

::DEVELOPER

CSIRO Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ChIPseqR

:: MORE INFORMATION

Citation

ChIPseqR: analysis of ChIP-seq experiments.
Humburg P, Helliwell CA, Bulger D, Stone G.
BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.

IsoCleft Finder – Detection and Analysis of Protein Binding-site Geometric and Chemical Similarities

IsoCleft Finder

:: DESCRIPTION

IsoCleft Finder is a web-based tool for the detection of local structural and chemical similarities between potential smallmolecule binding cavities and a non-redundant dataset of known small-molecule binding-sites.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Natalja Kurbatova, Matthieu Chartier, María Inés Zylber, Rafael Najmanovich (2013).
IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.
F1000 Research, 2:117

PIPE-SITES – Protein Binding Site Prediction

PIPE-SITES

:: DESCRIPTION

PIPE-Sites is a novel method for protein specific binding site prediction based on pairs of re-occurring polypeptide sequences, which have been previously shown to accurately predict protein-protein interactions

::DEVELOPER

the Parallel Computing and Data Science Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jun 2;12:225. doi: 10.1186/1471-2105-12-225.
Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences.
Amos-Binks A1, Patulea C, Pitre S, Schoenrock A, Gui Y, Green JR, Golshani A, Dehne F.

ProBiS 2.4.2 / ProBiS-ligands – Protein Binding Sites Detection

ProBiS 2.4.2 / ProBiS-ligands

:: DESCRIPTION

ProBiS is a web server and a computer program for the detection of structurally similar protein binding sites and pairwise local structural alignment.

The ProBiS-ligands web server predicts binding of ligands to a protein structure.

::DEVELOPER

ProBiS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Web browser that support HTML5.

:: DOWNLOAD

ProBiS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W436-40. doi: 10.1093/nar/gkq479. Epub 2010 May 26.
ProBiS: a web server for detection of structurally similar protein binding sites.
Konc J1, Janezic D.

J Comput Chem. 2012 Oct 15;33(27):2199-203. doi: 10.1002/jcc.23048. Epub 2012 Jun 20.
Parallel-ProBiS: fast parallel algorithm for local structural comparison of protein structures and binding sites.
Konc J1, Depolli M, Trobec R, Rozman K, Janežič D.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W215-20. doi: 10.1093/nar/gku460. Epub 2014 May 26.
ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.
Konc J1, Janežič D

Delila-Genome 1.0 – Analysis of Protein Binding Sites in complete Genome Sequences

Delila-Genome 1.0

:: DESCRIPTION

Delila-genome is a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices.

::DEVELOPER

Laboratories of Human Molecular Genetics and Genomic Disorders

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Delila-Genome

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2003 Sep 8;4:38. Epub 2003 Sep 8.
Genome-wide prediction, display and refinement of binding sites with information theory-based models.
Gadiraju S, Vyhlidal CA, Leeder JS, Rogan PK.

CanBind – Exploring Protein Binding sites Mutated in Cancer

CanBind

:: DESCRIPTION

CanBind is a pipeline to identify genes significantly mutated in cancer

::DEVELOPER

Dario Ghersi in Mona Singh’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

  CanBind

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Feb;42(3):e18. doi: 10.1093/nar/gkt1305. Epub 2013 Dec 19.
Interaction-based discovery of functionally important genes in cancers.
Ghersi D1, Singh M.

PINUP – Protein Binding Site Prediction with an Empirical Scoring Function

PINUP

:: DESCRIPTION

PINUP is a web servers for protein binding site prediction using an empirical scoring function.

::DEVELOPER

System Biology Laboratory Of Chi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Aug 7;34(13):3698-707. Print 2006.
Protein binding site prediction using an empirical scoring function.
Liang S1, Zhang C, Liu S, Zhou Y.

T-PIC – Determining DNA/protein Binding Sites from a ChIP-Seq Experiment

T-PIC

:: DESCRIPTION

T-PIC (Tree shape Peak Identification for ChIP-Seq) is a free software for determining DNA/protein binding sites from a ChIP-Seq experiment.

::DEVELOPER

Valerie Hower

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows
  • R package
  • Python

:: DOWNLOAD

 T-PIC

:: MORE INFORMATION

Citation

V. Hower, S.N. Evans, L. Pachter,
Shape-based peak identification for ChIP-Seq,
BMC Bioinformatics, 12:15 (2011). DOI:10.1186/1471-2105-12-15