Software
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License
All software on this site is released under the terms of the GNU Public License.
CAO
- Author
- Kuang Lin
- Description
- Contact mutation matrices.
- Download
- cao50.gz, cao80.gz, cao100.gz, cao120.gz, cao200.gz
- Reference
- 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]
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]
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.tar.gz
- SAP-1.1.1.tar.gz (released 04.02.10)
- SAP-1.1.0.tar.gz (released 15.07.09)
- Server
- SAP
- 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
- manuscript submitted
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 11:97 (20 February 2010). [open access]
- Pandini, A., Fornili, A., Fraternali, F. and Kleinjung, J., Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB Journal, online:fj.11-190868, 2011.
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 (in press). [early access]
