SOCKET 3.03 / iSocket 0.3.1 – Identifies Knobs-into-holes packing in Protein Structures

SOCKET 3.03 / iSocket 0.3.1

:: DESCRIPTION

The SOCKET program finds the Knobs-into-Holes mode of packing between alpha-helices which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script if required.

iSocket is a set of computational tools written in Python as an add-on to the ISAMBARD software suite.

::DEVELOPER

WOOLFSON lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler / Python

:: DOWNLOAD

SOCKET / iSocket

:: MORE INFORMATION

Citation

Heal JW, Bartlett GJ, Wood CW, Thomson AR, Woolfson DN.
Applying graph theory to protein structures: an Atlas of coiled coils.
Bioinformatics. 2018 Oct 1;34(19):3316-3323. doi: 10.1093/bioinformatics/bty347. PMID: 29722888; PMCID: PMC6157074.

Walshaw, J. & Woolfson, D.N. (2001)
Socket: a program for identifying and analysing coiled-coil motifs within protein structures.
J. Mol. Biol., 307 (5), 1427-1450

Phosfinder – Phosphate Binding Sites prediction on Protein Structures

Phosfinder

:: DESCRIPTION

Phosfinder is a bioinformatic web server for the prediction of phosphate-binding sites in protein structures.

::DEVELOPER

Phosfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82. doi: 10.1093/nar/gkr389. Epub 2011 May 26.
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.
Parca L1, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2011 Mar;39(4):1231-42. doi: 10.1093/nar/gkq987. Epub 2010 Oct 24.
Phosphate binding sites identification in protein structures.
Parca L1, Gherardini PF, Helmer-Citterich M, Ausiello G.

iPBA – Protein Structures Mining and Superimposition

iPBA

:: DESCRIPTION

iPBA is a tool for protein structures mining and superimposition based on similarity in the local backbone conformation.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

iPBA: a tool for protein structure comparison using sequence alignment strategies.
Gelly JC, Joseph AP, Srinivasan N, de Brevern AG.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W18-23. doi: 10.1093/nar/gkr333.

PocketAlign – Aligning Binding Sites in Protein Structures

PocketAlign

:: DESCRIPTION

PocketAlign is a web server of comparison of binding sites helps identify functional similarities and also identify drug cross-reactivities

::DEVELOPER

Chandra lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 Jul 25;51(7):1725-36. doi: 10.1021/ci200132z. Epub 2011 Jun 21.
PocketAlign a novel algorithm for aligning binding sites in protein structures.
Yeturu K, Chandra N.

Frag’r’Us – Extract and Characterize Supersecondary, or Smotifs from Protein Structures

Frag’r’Us

:: DESCRIPTION

Frag’R’Us is a web application designed to sample alternative protein backbone conformations in loop regions using the geometrical constrains of smotifs

::DEVELOPER

Bioinformatics Lab :: IBERS :: Aberystwyth University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Server

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 21.
Frag’r’Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design.
Bonet J1, Segura J, Planas-Iglesias J, Oliva B, Fernandez-Fuentes N.

Raphael 1.0 – Determination of Periodicity in Protein Structures

Raphael 1.0

:: DESCRIPTION

RAPHAEL is a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Dec 15;28(24):3257-64. doi: 10.1093/bioinformatics/bts550. Epub 2012 Sep 8.
RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures.
Walsh I1, Sirocco FG, Minervini G, Di Domenico T, Ferrari C, Tosatto SC.