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License

All software on this site is released under the terms of the GNU Public License.

CAO

The CAO principle has been incorporated into the STRIKE program with reduced complexity and better parametrisation.

Reference 
Kemena, C., Taly, J.-F., Kleinjung, J., Notredame, C., STRIKE: Evaluation of Protein Multiple Sequence Alignments using a Single Three Dimensional Structure. Bioinformatics 27 (2011) 3385-3391.
Lin, K., Kleinjung, J., Taylor, W.R. and Heringa, J., Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. Comput Biol Chem. 27 (2003) 93-102. [PubMed]
Kleinjung, J., Romein, J., Lin, K. and Heringa, J., Contact-based sequence alignment. Nucleic Acids Res. 32 (2004) 2464-2473. [open access]

Contact-based Domain Predictors

Author 
Michael Sadowski
Description 
Prediction of Protein Domain Boundaries From Inverse Covariances.
Download 
contact_domain_prediction.tar.gz
Reference 
"Prediction of Protein Domain Boundaries From Inverse Covariances" (Sadowski, 2012) submitted to Proteins.

De Novo Backbone Scaffolds

Author 
James MacDonald
Description 
Design decoy sets as described in the paper.
Download 
high quality decoys2, low quality decoys, random protein controls, real2 protein controls, real protein controls
Reference 
MacDonald, J.T., Maksimiak, K., Sadowski, M.I. and Taylor, W.R. De novo backbone scaffolds for protein design. Proteins 78 (2009) 1311-1325. [PubMed]

GSA Tools

Author 
Alessandro Pandini
Description 
Detection of allosteric motion in protein ensembles.
Download

GSATools

KNOT

Author 
Willie Taylor
Description 
Detection of knots in protein folds.
Download 
Server 
in preparation
Reference 
Taylor, W.R., A deeply knotted protein structure and how it might fold. Nature 406 (2000) 916-919. [PubMed]

MinSet

Author 
Alessandro Pandini and Jens Kleinjung
Description 
Optimised SCOP database subsets for benchmarking and parametrisation.
Project Funding
European Science Foundation, Frontiers of Functional Genomics
Download 
Code available from authors; release in preparation.
Server 
MinSet
Reference 
Pandini, A., Bonati, L., Fraternali, F. and Kleinjung, J., MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database. Bioinformatics 23 (2007) 515-516. [PubMed]

NetFeat

Author 
Jens Kleinjung, Franca Fraternali, Luis Fernandes, Alessia Annibale, Ton Coolen
Description 
Analysis of interaction networks via information-theoretic tools.
Project Funding
MRC, EPSRC, Leverhulme Trust
Download 
Code available from authors; release in preparation.
Server 
NetFeat (not yet functional)
Reference 
Fernandes, L P, Annibale, A, Kleinjung, J, Coolen, A C C, Fraternali, F - Protein networks reveal detection bias and species consistency in information-theoretic analyses. PLoS ONE 5:e12083, 2010. [open access]

OPTICS

Author 
Jens Kleinjung and Alessandro Pandini
Description 
Clustering by single-linkage point ordering.
Project Funding
EU Marie Curie Fellowship, MRC
Download
Reference 
Pandini, A, Fornili, A, Kleinjung, J - Structural alphabets derived from attractors in conformational space BMC Bioinformatics 11:97 (20 February), 2010. [open access]

POPS*

Author 
Franca Fraternali, Luigi Cavallo, Jens Kleinjung et al.
Description
Fast and accurate computation of surface areas of proteins and nucleic acids.
Download 
Server 
POPS : protein or RNA/DNA surface area
Server 
POPSCOMP : protein or RNA/DNA complex analysis
Reference 
Fraternali, F. and Cavallo, L., Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Research 30 (2002) 2950-2960. [open access]

POPSCOMP

Author 
Franca Fraternali and Jens Kleinjung
Description 
Computation of complex interaction surfaces via buried surface areas.
Download 
Code available from authors; release in preparation.
Server 
POPSCOMP
Reference 
Kleinjung, J. and Fraternali, F., POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Research 33 (2005) W342-W346. [open access]

SAP

Author 
Willie Taylor
Description
Pairwise protein structure alignment via double dynamic programming.
Download 
Server 
SAP : pairwise protein structure alignment
Reference 
Taylor, W.R., Protein structure comparison using iterated double dynamic programming. Protein Sci. 8 (1999) 654-665. [PubMed]
Taylor W.R., Protein structure comparison using SAP. Methods Mol. Biol. 143 (2000) 19-32. [PubMed]

Solvent Forces

Author 
Franca Fraternali, Walter R.P. Scott, Wilfred F. van Gunsteren, Jens Kleinjung
Description 
Explicit solvent (water) forces of 188 protein domains in Molecular Dynamics simulations. For more information see Solvent_Forces.
Download 
Reference 
Kleinjung, J and Scott, W R P and Allison, J R and van Gunsteren, W F and Fraternali, F, Implicit solvation parameters derived from explicit water forces in large-scale Molecular Dynamics simulations. J Chem Theor Comp 2012; 8:2391–2403. [open access]

StickSAP

Author 
Michael Sadowski and Willie Taylor
Description
Source code, utility scripts and data for matching ideal forms to PDB structures and deriving topology strings. Includes matches to SCOP 1.73.
Download 
Reference 
Taylor W.R. (2002) A "periodic table" for protein structures. Nature 416: 657-60. [PubMed]
Sadowski M.I., Taylor W.R. (2010) On the evolutionary origins of "Fold Space Continuity": A study of topological convergence and divergence in mixed alpha-beta domains. J. Struct. Biol 172:244-52. [PubMed]

Structural Alphabet M32K25

Author 
Alessandro Pandini, Arianna Fornili, Franca Fraternali and Jens Kleinjung
Description
A structural alphabet for the description of protein structures and their dynamics.
Download 
Server
PdbEncode
Reference 
Pandini, A., Fornili, A. and Kleinjung, J., Structural alphabets derived from attractors in conformational space. BMC Bioinformatics 2010 11:97. [open access]
Pandini, A., Fornili, A., Fraternali, F. and Kleinjung, J., Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J. 2012 26(2):868-881. [open access]

Supplementary Info

Paper Protein Sci. 2012 21:299-305.

Author 
Willie Taylor, David Jones and Michael Sadowski
Description 
Tar file
Download 

Paper Bioinformatics 2012 28:1209-15.

Author 
Michael Sadowski and Willie Taylor
Description 
Pairwise structural alignment data
Download 

TdG12 - Distribution of Selection Coefficients

Author 
Asif Tamuri, Mario Dos Reis and Richard Goldstein
Description
Program for estimating the distribution of selection coefficients (fitness effects) from phylogenetic data using a site-wise mutation-selection model.
Download 
tdg12.zip (released 11.01.12)
Source and updates
github tamuri/tdg12
Reference 
Tamuri AU, dos Reis M, Goldstein RA. Using Site-wise Mutation-Selection Models to Estimate the Distribution of Selection Coefficients from Phylogenetic Data. Genetics. 2012 190(3):1101-1115. [open access]
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