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Contents 1 License 2 CAO 3 Contact-based Domain Predictors 4 De Novo Backbone Scaffolds 5 KNOT 6 MinSet 7 NetFeat 8 OPTICS 9 POPS* 10 POPSCOMP 11 SAP 12 Solvent Forces 13 StickSAP 14 Structural Alphabet M32K25 15 Supplementary Info 16 TdG12 - Distribution of Selection Coefficients

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]

KNOT

Author 

Willie Taylor

Description 

Detection of knots in protein folds.

Download 

• latest release KNOT.tgz
• KNOT-1.0.0.tgz

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

• latest release optics.tar.gz
• optics-1.0.1.tar.gz (released 30.07.12)

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 

• latest release pops.tar.gz
• pops-1.5.3.tar.gz (released 02.05.12)

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 

• latest release sap.tgz
• sap-1.1.3.tgz (released 25.09.12)

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 

• ExplicitWaterForces.tar.bz2
• ListOfDomains.txt

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 

• form_match_data.tar.gz (released 27.01.11)
• sticksap.tar.gz (released 27.01.11)

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 

• fragment alphabet M32K25.pdb (released 11.03.10)
• data set MK.dataset.txt (released 11.03.10)
• test set MK.testset.txt (released 11.03.10)

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

Author 

Willie Taylor, David Jones and Michael Sadowski

Description

Supplementary info for paper submitted to Protein Science October 2011

Download 

• Tar file [1]

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]