MODELLER

• MODELLER is used for homology or comparative modeling of protein three-dimensional structures.

Referência(s):

1. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

2. B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., 5.6.1-5.6.32, 2014.

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Clustal Omega

• "The last alignment program you'll ever need."

Referência(s):

1. Higgins,D.G. and Sharp,P.M. (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene, 73, 237-244.

2. Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.

3. Higgins DG, Thompson JD, Gibson TJ. (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol., 266, 383-402.

4. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology7:539 doi:10.1038/msb.2011.75

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MUSCLE

• MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.

Referência(s):

1. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797

2. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, (5) 113

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Seaview

• SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

Referência(s):

1. Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.

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Coot (for Windows)

• Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Referência(s):

1. P. Emsley; B. Lohkamp; W.G. Scott; Cowtan (2010). Features and development of Coot. Acta Crystallographica. D66: 486–501.

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BLAST

• BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

Referência(s):

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

2. Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.

3. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.

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Threader

• Threading is one of the very few methods available which can predict the fold for a protein in the absence of an evolutionary relationship.

Referência(s):

1. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) A new approach to protein fold recognition. Nature. 358, 86-89.

2. Jones, D.T. (1998) THREADER : Protein Sequence Threading by Double Dynamic Programming. (in) Computational Methods in Molecular Biology. Steven Salzberg, David Searls, and Simon Kasif, Eds. Elsevier Science. Chapter 13.

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PSIPRED

• The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location. Users can submit a protein sequence, perform the predictions of their choice and receive the results of the prediction via e-mail or the web.

Referência(s):

1. Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.

2. Buchan DWA, Minneci F, Nugent TCO, Bryson K, Jones DT. (2013). Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Research . 41 (W1): W340-W348.

3. Jones DT. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287: 797-815.

4. Lobley, A., Sadowski, M.I. & Jones, D.T. (2009) pGenTHREADER and pDomTHREADER: New Methods For Improved Protein Fold Recognition and Superfamily Discrimination.Bioinformatics. 25, 1761-1767.

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jsPISA

• jsPISA is an interactive web tool for the calculation of macromolecular surfaces and interfaces, assessment of their properties and inference on probable macromolecular assemblies (complexes) from coordinate data, typically delivered by crystallographic X-ray experiment.

Referência(s):

1. E. Krissinel and K. Henrick (2007) Inference of macromolecular assemblies from crystalline state, J. Mol. Biol. 372, 774-797.

2. E. Krissinel (2015) Stock-based detection of protein oligomeric states in jsPISA, Nucl. Acids Res., DOI:10.1093/nar/gkv314.

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QMEAN

• QMEAN is a composite scoring function which is able to derive both global (i.e. for the entire structure) and local (i.e. per residue) error estimates on the basis of one single model.

Referência(s):

1. Benkert, P., Tosatto, S.C.E. and Schomburg, D. (2008). "QMEAN: A comprehensive scoring function for model quality assessment." Proteins: Structure, Function, and Bioinformatics, 71(1):261-277.

2. Benkert, P., Biasini, M. and Schwede, T. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics (2010). doi: 10.1093/bioinformatics/btq662

3. Benkert, P., Schwede, T. and Tosatto, S.C.E. (2009). "QMEANclust: Estimation of protein model quality by # combining a composite scoring function with structural density information." BMC Struct Biol. 2009 May 20;9:35.

4. Benkert P, Künzli M, Schwede T. (2009). "QMEAN Server for Protein Model Quality Estimation." Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W510-4.

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