|
|||||||
ReferencesAdamczak R, Porollo A, Meller J. 2004. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 56(4):753-67. Adamczak R, Porollo A, Meller J. 2005. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59(3):467-75. Bao L, Zhou M, Cui Y. 2005. nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Res 33(Web Server issue):W480-2. Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N. 2004. ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20(8):1322-4. Capriotti E, Calabrese R, Casadio R. 2006. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 22(22):2729-34. Capriotti E, Fariselli P, Calabrese R, Casadio R. 2005a. Predicting protein stability changes from sequences using support vector machines. Bioinformatics 21 Suppl 2:ii54-8. Capriotti E, Fariselli P, Casadio R. 2005b. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33(Web Server issue):W306-10. Cavallo A, Martin AC. 2005. Mapping SNPs to protein sequence and structure data. Bioinformatics 21(8):1443-50. Cheng J, Randall A, Baldi P. 2006. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62(4):1125-32. Cheng J, Randall AZ, Sweredoski MJ, Baldi P. 2005. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 33(Web Server issue):W72-6. Coeytaux K, Poupon A. 2005. Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics 21(9):1891-900. Conchillo-Sole O, de Groot NS, Aviles FX, Vendrell J, Daura X, Ventura S. 2007. AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides. BMC Bioinformatics 8:65. Dantzer J, Moad C, Heiland R, Mooney S. 2005. MutDB services: interactive structural analysis of mutation data. Nucleic Acids Res 33(Web Server issue):W311-4. Davis IW, Murray LW, Richardson JS, Richardson DC. 2004. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32(Web Server issue):W615-9. DeLano W. 2002. The PyMOL Molecular Graphics System. Palo Alto, CA, USA: DeLano Scientific. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 15(2):330-40. Dosztanyi Z, Csizmok V, Tompa P, Simon I. 2005. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21(16):3433-4. Dosztanyi Z, Fiser A, Simon I. 1997. Stabilization centers in proteins: identification, characterization and predictions. J Mol Biol 272(4):597-612. Dosztanyi Z, Magyar C, Tusnady G, Simon I. 2003. SCide: identification of stabilization centers in proteins. Bioinformatics 19(7):899-900. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792-7. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. 2004. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22(10):1302-6. Ferrer-Costa C, Gelpi JL, Zamakola L, Parraga I, de la Cruz X, Orozco M. 2005. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 21(14):3176-8. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL and others. 2008. The Pfam protein families database. Nucleic Acids Res 36(Database issue):D281-8. Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. 2006. FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics 22(23):2948-9. Gilis D, Rooman M. 2000. PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein Eng 13(12):849-56. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. 2003. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19(1):163-4. Guerois R, Nielsen JE, Serrano L. 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320(2):369-87. Higa RH, Montagner AJ, Togawa RC, Kuser PR, Yamagishi ME, Mancini AL, Pappas G, Jr., Miura RT, Horita LG, Neshich G. 2004. ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics 20(12):1983-5. Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T. 2007. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics 23(16):2046-53. Huang L-T, Gromiha MM, Ho S-Y. 2007. iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics 23(10):1292-1293. Ishida T, Kinoshita K. 2007. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 35(Web Server issue):W460-4. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33(2):511-8. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059-66. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. 2005. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33(Web Server issue):W299-302. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R and others. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947-8. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. 2003a. Protein disorder prediction: implications for structural proteomics. Structure 11(11):1453-9. Linding R, Russell RB, Neduva V, Gibson TJ. 2003b. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 31(13):3701-8. Liu J, Rost B. 2003. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res 31(13):3833-5. Lovell SC, Davis IW, Arendall WB, 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. 2003. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50(3):437-50. Magyar C, Gromiha MM, Pujadas G, Tusnady GE, Simon I. 2005. SRide: a server for identifying stabilizing residues in proteins. Nucleic Acids Res 33(Web Server issue):W303-5. Masso M, Vaisman, II. 2008. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. Bioinformatics 24(18):2002-9. Ng PC, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res 11(5):863-74. Obradovic Z, Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK. 2003. Predicting intrinsic disorder from amino acid sequence. Proteins 53 Suppl 6:566-72. Parthiban V, Gromiha MM, Schomburg D. 2006. CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res 34(Web Server issue):W239-42. Pei J, Kim BH, Tang M, Grishin NV. 2007. PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res 35(Web Server issue):W649-52. Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z. 2005. Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol 3(1):35-60. Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg EH, Man O, Beckmann JS, Silman I, Sussman JL. 2005. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21(16):3435-8. Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, Hamodrakas S, Sander C, Ouzounis CA. 2000. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics 16(10):915-22. Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30(17):3894-900. Shen B, Vihinen M. 2003. RankViaContact: ranking and visualization of amino acid contacts. Bioinformatics 19(16):2161-2. Shen B, Vihinen M. 2004. Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain. Protein Eng Des Sel 17(3):267-76. Shimizu K, Hirose S, Noguchi T. 2007a. POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics 23(17):2337-8. Shimizu K, Muraoka Y, Hirose S, Tomii K, Noguchi T. 2007b. Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinformatics 8:78. Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M. 1999. Automated analysis of interatomic contacts in proteins. Bioinformatics 15(4):327-32. Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M. 2005. SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res 33(Web Server issue):W39-43. Stenson PD, Ball E, Howells K, Phillips A, Mort M, Cooper DN. 2008. Human Gene Mutation Database: towards a comprehensive central mutation database. J Med Genet 45(2):124-6. Su CT, Chen CY, Hsu CM. 2007. iPDA: integrated protein disorder analyzer. Nucleic Acids Res 35(Web Server issue):W465-72. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. 2003. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13(9):2129-41. 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(22):4673-80. Thompson JD, Plewniak F, Poch O. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27(13):2682-90. Trovato A, Seno F, Tosatto SC. 2007. The PASTA server for protein aggregation prediction. Protein Eng Des Sel 20(10):521-3. Wagner M, Adamczak R, Porollo A, Meller J. 2005. Linear regression models for solvent accessibility prediction in proteins. J Comput Biol 12(3):355-69. Wallace IM, O’Sullivan O, Higgins DG, Notredame C. 2006. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res 34(6):1692-9. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337(3):635-45. Wootton JC. 1994. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 18(3):269-85. Word JM, Bateman RC, Jr., Presley BK, Lovell SC, Richardson DC. 2000. Exploring steric constraints on protein mutations using MAGE/PROBE. Protein Sci 9(11):2251-9. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. 1999. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285(4):1711-33. Vucetic S, Brown CJ, Dunker AK, Obradovic Z. 2003. Flavors of protein disorder. Proteins 52(4):573-84. Vullo A, Bortolami O, Pollastri G, Tosatto SC. 2006. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res 34(Web Server issue):W164-8. Yang ZR, Thomson R, McNeil P, Esnouf RM. 2005. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21(16):3369-76. Yin S, Ding F, Dokholyan NV. 2007. Eris: an automated estimator of protein stability Nature Methods 4:466-467. Yin S, Ding F, Dokholyan NV. 2007. Modeling backbone flexibility improves protein stability estimation. Structure 15:1567-1576. Yue P, Melamud E, Moult J. 2006. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 7:166. Zhou H, Zhou Y. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11(11):2714-26. |
|||||||
©
IBT Bioinformatics 2008-2012
|
|||||||