Analyzing effects of naturally occurring missense mutations

Computational and Mathematical Methods in Medicine

Volumn 2012, Issue , 2012, Pages

  Zhang, Zhe ^a,b   Miteva, Maria A ^b   Wang, Lin ^a   Alexov, Emil ^a  

^a CLEMSON UNIVERSITY   (United States)

^b UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; NUCLEOTIDES; THREE DIMENSIONAL COMPUTER GRAPHICS;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; MOLECULAR MECHANISM; PROTEIN-PROTEIN INTERACTIONS; SINGLE-NUCLEOTIDE POLYMORPHISMS; SINGLE-POINT MUTATION; STANDALONE APPLICATIONS; UNDERLYING PRINCIPLES;

PROTEINS;

ELECTRON TRANSFERRING FLAVOPROTEIN; NUCLEOTIDE; PROTEIN; SODIUM IODIDE SYMPORTER; SPERMINE SYNTHASE; MUTANT PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CELLULAR DISTRIBUTION; DIMERIZATION; GENE SEQUENCE; HYDROGEN BOND; HYDROPHOBICITY; MISSENSE MUTATION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODEL; MONTE CARLO METHOD; PHYLOGENY; PROTEIN AGGREGATION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; WILD TYPE; ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BINDING SITE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETIC DATABASE; GENETICS; HUMAN; KINETICS; METABOLISM; PROTEIN MULTIMERIZATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BINDING SITES; COMPUTER SIMULATION; DATABASES, GENETIC; HUMANS; KINETICS; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTANT PROTEINS; MUTATION, MISSENSE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN FOLDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; SPERMINE SYNTHASE;

EID: 84861052952     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1155/2012/805827     Document Type: Review

References (184)

1. Taillon-Miller P., Gu Z., Li Q., Hillier L., Kwok P. Y., Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms Genome Research 1998 8 7 748 754 (Pubitemid 28403175)
2. Mooney S., Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis Briefings in Bioinformatics 2005 6 1 44 56 (Pubitemid 40528579)
3. Hagmann M., Human genome. A good SNP may be hard to find Science 1999 285 5424 21 22
4. Strachan T., Read A. P., Human Molecular Genetics 1999
5. Zhang Z., Teng S., Wang L., Schwartz C. E., Alexov E., Computational analysis of missense mutations causing Snyder-Robinson syndrome Human Mutation 2010 31 9 1043 1049
6. Zhang Z., Norris J., Schwartz C., Alexov E., In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase PLoS One 2011 6 5
7. Akhavan S., Miteva M. A., Villoutreix B. O., Venisse L., Peyvandi F., Mannucci P. M., Guillin M. C., Bezeaud A., A critical role for Gly25 in the B chain of human thrombin Journal of Thrombosis and Haemostasis 2005 3 1 139 145 (Pubitemid 41647126)
8. Miteva M. A., Brugge J. M., Rosing J., Nicolaes G. A. F., Villoutreix B. O., Theoretical and experimental study of the D2194G mutation in the C2 domain of coagulation factor V Biophysical Journal 2004 86 1, part 1 488 498 (Pubitemid 38067478)
9. Steen M., Miteva M., Villoutreix B. O., Yamazaki T., Dahlback B., Factor V new brunswick: Ala221Val associated with FV deficiency reproduced in vitro and functionally characterized Blood 2003 102 4 1316 1322 (Pubitemid 36988038)
10. Witham S., Takano K., Schwartz C., Alexov E., A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics Proteins 2011 79 8 2444 2454
11. Teng S., Madej T., Panchenko A., Alexov E., Modeling effects of human single nucleotide polymorphisms on protein-protein interactions Biophysical Journal 2009 96 6 2178 2188
12. Dobson C. M., Protein folding and misfolding Nature 2003 426 6968 884 890 (Pubitemid 38056880)
13. Venkatesan R. N., Treuting P. M., Fuller E. D., Goldsby R. E., Norwood T. H., Gooley T. A., Ladiges W. C., Preston B. D., Loeb L. A., Mutation at the polymerase active site of mouse DNA polymerase increases genomic instability and accelerates tumorigenesis Molecular and Cellular Biology 2007 27 21 7669 7682 (Pubitemid 350033672)
14. Elles L. M. S., Uhlenbeck O. C., Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype Nucleic Acids Research 2008 36 1 41 50
15. Wright J. D., Lim C., Mechanism of DNA-binding loss upon single-point mutation in p53 Journal of Biosciences 2007 32 5 827 839 (Pubitemid 47435515)
16. Kwa L. G., Wegmann D., Brugger B., Wieland F. T., Wanner G., Braun P., Mutation of a single residue, -glutamate-20, alters protein-lipid interactions of light harvesting complex II Molecular Microbiology 2008 67 1 63 77 (Pubitemid 350231135)
17. Kariya Y., Tsubota Y., Hirosaki T., Mizushima H., Puzon-McLaughlin W., Takada Y., Miyazaki K., Differential regulation of cellular adhesion and migration by recombinant laminin-5 forms with partial deletion or mutation within the G3 domain of 3 chain Journal of Cellular Biochemistry 2003 88 3 506 520 (Pubitemid 36158272)
18. Tiede S., Cantz M., Spranger J., Braulke T., Missense mutation in the N-acetylglucosamine-1-phosphotransferase gene (GNPTA) in a patient with mucolipidosis II induces changes in the size and cellular distribution of GNPTG Human Mutation 2006 27 8 830 831
19. Krumbholz M., Koehler K., Huebner A., Cellular localization of 17 natural mutant variants of ALADIN protein in triple A syndromeshedding light on an unexpected splice mutation Biochemistry and Cell Biology 2006 84 2 243 249 (Pubitemid 43946035)
20. Hanemann C. O., D'Urso D., Gabreels-Festen A. A. W. M., Muller H. W., Mutation-dependent alteration in cellular distribution of peripheral myelin protein 22 in nerve biopsies from Charcot-Marie-Tooth type 1A Brain 2000 123 5 1001 1006 (Pubitemid 30224195)
21. Sherry S. T., Ward M. H., Kholodov M., Baker J., Phan L., Smigielski E. M., Sirotkin K., DbSNP: the NCBI database of genetic variation Nucleic Acids Research 2001 29 1 308 311 (Pubitemid 32054478)
22. Fredman D., Munns G., Rios D., Sjoholm F., Siegfried M., Lenhard B., Lehvaslaiho H., Brookes A. J., HGVbase: a curated resource describing human DNA variation and phenotype relationships Nucleic Acids Research 2004 32 D516 D519
23. Stitziel N. O., Binkowski T. A., Tseng Y. Y., Kasif S., Liang J., topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association Nucleic Acids Research 2004 32 Database issue D520 D522
24. Hamosh A., Scott A. F., Amberger J., Valle D., McKusick V. A., Online mendelian inheritance in man (OMIM) Human Mutation 2000 15 1 57 61 (Pubitemid 30036170)
25. Hamosh A., Scott A. F., Amberger J., Bocchini C., Valle D., McKusick V. A., Onlined mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders Nucleic Acids Research 2002 30 1 52 55 (Pubitemid 34679502)
26. Hamosh A., Scott A. F., Amberger J. S., Bocchini C. A., McKusick V. A., Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders Nucleic Acids Research 2005 33 D514 D517
27. Teng S., Michonova-Alexova E., Alexov E., Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions Current Pharmaceutical Biotechnology 2008 9 2 123 133 (Pubitemid 351513490)
28. Sayers E. W., Barrett T., Benson D. A., Bolton E., Bryant S. H., Canese K., Chetvernin V., Church D. M., DiCuccio M., Federhen S., Feolo M., Fingerman I. M., Geer L. Y., Helmberg W., Kapustin Y., Landsman D., Lipman D. J., Lu Z., Madden T. L., Madej T., Maglott D. R., Marchler-Bauer A., Miller V., Mizrachi I., Ostell J., Panchenko A., Phan L., Pruitt K. D., Schuler G. D., Sequeira E., Sherry S. T., Shumway M., Sirotkin K., Slotta D., Souvorov A., Starchenko G., Tatusova T. A., Wagner L., Wang Y., Wilbur W. J., Yaschenko E., Ye J., Database resources of the national center for biotechnology information Nucleic Acids Research 2011 39 Database issue supplement 1 D38 D51
29. Smigielski E. M., Sirotkin K., Ward M., Sherry S. T., dbSNP: a database of single nucleotide polymorphisms Nucleic Acids Research 2000 28 1 352 355 (Pubitemid 30047805)
30. Sherry S. T., Ward M., Sirotkin K., dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation Genome Research 1999 9 8 677 679 (Pubitemid 29412785)
31. Cooper D. N., Ball E. V., Krawczak M., The human gene mutation database Nucleic Acids Research 1998 26 1 285 287 (Pubitemid 28291543)
32. Stitziel N. O., Tseng Y. Y., Pervouchine D., Goddeau D., Kasif S., Liang J., Structural location of disease-associated single-nucleotide polymorphisms Journal of Molecular Biology 2003 327 5 1021 1030 (Pubitemid 36363709)
33. Altman R. B., PharmGKB: a logical home for knowledge relating genotype to drug response phenotype Nature Genetics 2007 39 4, article 426
34. Packer B. R., Yeager M., Burdett L., Welch R., Beerman M., Qi L., Sicotte H., Staats B., Acharya M., Crenshaw A., Eckert A., Puri V., Gerhard D. S., Chanock S. J., SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes Nucleic acids research. 2006 34 D617 D621
35. Bidwell J., Keen L., Gallagher G., Kimberly R., Huizinga T., McDermott M. F., Oksenberg J., McNicholl J., Pociot F., Hardt C., D'Alfonso S., Cytokine gene polymorphism in human disease: on-line databases Genes and Immunity 1999 1 1 3 19 (Pubitemid 129622776)
36. Bash P. A., Singh U. C., Langridge R., Kollman P. A., Free energy calculations by computer simulation Science 1987 236 4801 564 568 (Pubitemid 17069921)
37. Duan Y., Kollman P. A., Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Science 1998 282 5389 740 744 (Pubitemid 28489385)
38. Khare S. D., Caplow M., Dokholyan N. V., FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis Amyloid 2006 13 4 226 235 (Pubitemid 44764462)
39. Kuhlman B., Baker D., Native protein sequences are close to optimal for their structures Proceedings of the National Academy of Sciences of the United States of America 2000 97 19 10383 10388
40. Lee C., Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the Ala→Val mutants of T4 lysozyme Folding and Design 1996 1 1 1 12 (Pubitemid 126748153)
41. Lee C., Levitt M., Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core Nature 1991 352 6334 448 451 (Pubitemid 21896746)
42. Miyazawa S., Jernigan R. L., Protein stability for single substitution mutants and the extent of local compactness in the denatured state Protein Engineering 1994 7 10 1209 1220 (Pubitemid 24319399)
43. Pitera J. W., Kollman P. A., Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides Proteins 2000 41 3 385 397
44. Prevost M., Wodak S. J., Tidor B., Karplus M., Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96→Ala mutation in barnase Proceedings of the National Academy of Sciences of the United States of America 1991 88 23 10880 10884 (Pubitemid 21915942)
45. Tidor B., Simulation analysis of the stability mutant R96h of T4 lysozyme Biochemistry 1991 30 13 3217 3228
46. Vorobjev Y. N., Hermans J., ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model Biophysical Chemistry 1999 78 1-2 195 205 (Pubitemid 29206666)
47. Ben-Naim A., Statistical potentials extracted from protein structures: are these meaningful potentials? Journal of Chemical Physics 1997 107 9 3698 3706 (Pubitemid 127635865)
48. Thomas P. D., Dill K. A., Statistical potentials extracted from protein structures: how accurate are they? Journal of Molecular Biology 1996 257 2 457 469 (Pubitemid 26114046)
49. Gilis D., Rooman M., Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials Journal of Molecular Biology 1996 257 5 1112 1126 (Pubitemid 26117093)
50. Gilis D., Rooman M., Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence Journal of Molecular Biology 1997 272 2 276 290 (Pubitemid 27397351)
51. Gilis D., Rooman M., PoPMuSiC, an algorithm for predicting protein mutant stability changes. Application to prion proteins Protein Engineering 2000 13 12 849 856 (Pubitemid 32233944)
52. Hoppe C., Schomburg D., Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential Protein Science 2005 14 10 2682 2692 (Pubitemid 41395594)
53. Ota M., Isogai Y., Nishikawa K., Knowledge-based potential defined for a rotamer library to design protein sequences Protein Engineering 2001 14 8 557 564 (Pubitemid 32959480)
54. Topham C. M., Srinivasan N., Blundell T. L., Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables Protein Engineering 1997 10 1 7 21 (Pubitemid 27073347)
55. Zhou H., Zhou Y., Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction Protein Science 2002 11 11 2714 2726 (Pubitemid 35191145)
56. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., The protein data bank Nucleic Acids Research 2000 28 1 235 242 (Pubitemid 30047768)
57. Bordner A. J., Abagyan R. A., Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations Proteins 2004 57 2 400 413 (Pubitemid 39223745)
58. Domingues H., Peters J., Schneider K. H., Apeler H., Sebald W., Oschkinat H., Serrano L., Improving the refolding yield of interleukin-4 through the optimization of local interactions Journal of Biotechnology 2000 84 3 217 230
59. Munoz V., Serrano L., Development of the multiple sequence approximation within the AGADIR Model of -helix formation: comparison with zimm-bragg and lifson-roig formalisms Biopolymers 1997 41 5 495 509
60. Takano K., Ota M., Ogasahara K., Yamagata Y., Nishikawa K., Yutani K., Experimental verification of the stability profile of mutant protein (SPMP) data using mutant human lysozymes Protein Engineering 1999 12 8 663 672 (Pubitemid 29425551)
61. Verma D., Jacobs D. J., Livesay D. R., Predicting the melting point of human C-type lysozyme mutants Current Protein and Peptide Science 2010 11 7 562 572
62. Villegas V., Viguera A. R., Aviles F. X., Serrano L., Stabilization of proteins by rational design of -helix stability using helix/coil transition theory Folding and Design 1996 1 1 29 34 (Pubitemid 126748156)
63. Schymkowitz J., Borg J., Stricher F., Nys R., Rousseau F., Serrano L., The FoldX web server: an online force field Nucleic Acids Research 2005 33 2 W382 W388
64. Guerois R., Nielsen J. E., Serrano L., Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations Journal of Molecular Biology 2002 320 2 369 387 (Pubitemid 34722226)
65. Zhang Z., Wang L., Gao Y., Zhang J., Zhenirovskyy M., Alexov E., Predicting folding free energy changes upon single point mutations Bioinformatics 2012 28 5 664 671
66. Capriotti E., Fariselli P., Casadio R., A neural-network-based method for predicting protein stability changes upon single point mutations Bioinformatics 2004 20 supplement 1 i63 i68
67. Casadio R., Compiani M., Fariselli P., Vivarelli F., Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks Proceedings International Conference on Intelligent Systems for Molecular Biology 1995 3 81 88
68. Frenz C. M., Neural network-based prediction of mutation-induced protein stability changes in staphylococcal nuclease at 20 residue positions Proteins 2005 59 2 147 151 (Pubitemid 40471555)
69. Joachims T., Learning to Classify Text Using Support Vector Machines 2002 Springer
70. Masso M., Vaisman I. I., Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis Bioinformatics 2008 24 18 2002 2009
71. Capriotti E., Fariselli P., Calabrese R., Casadio R., Predicting protein stability changes from sequences using support vector machines Bioinformatics 2005 21 supplement 2 ii54 ii58
72. Capriotti E., Fariselli P., Casadio R., I-mutant2.0: predicting stability changes upon mutation from the protein sequence or structure Nucleic Acids Research 2005 33 2 W306 W310
73. Yamada Y., Banno Y., Yoshida H., Kikuchi R., Akao Y., Murate T., Nozawa Y., Catalytic inactivation of human phospholipase D2 by a naturally occurring Gly901Asp mutation Archives of Medical Research 2006 37 6 696 699 (Pubitemid 43975165)
74. Stevanin G., Hahn V., Lohmann E., Bouslam N., Gouttard M., Soumphonphakdy C., Welter M. L., Ollagnon-Roman E., Lemainque A., Ruberg M., Brice A., Durr A., Mutation in the catalytic domain of protein kinase C and extension of the phenotype associated with spinocerebellar ataxia type 14 Archives of Neurology 2004 61 8 1242 1248 (Pubitemid 39062678)
75. Takamiya O., Seta M., Tanaka K., Ishida F., Human factor VII deficiency caused by S339C mutation located adjacent to the specificity pocket of the catalytic domain Clinical and Laboratory Haematology 2002 24 4 233 238 (Pubitemid 34989254)
76. Koukouritaki S. B., Poch M. T., Henderson M. C., Siddens L. K., Krueger S. K., Vandyke J. E., Williams D. E., Pajewski N. M., Wang T., Hines R. N., Identification and functional analysis of common human flavin-containing monooxygenase 3 genetic variants Journal of Pharmacology and Experimental Therapeutics 2007 320 1 266 273 (Pubitemid 46028481)
77. de Cristofaro R., Carotti A., Akhavan S., Palla R., Peyvandi F., Altomare C., Mannucci P. M., The natural mutation by deletion of Lys9 in the thrombin A-chain affects the PK a value of catalytic residues, the overall enzyme's stability and conformational transitions linked to Na + binding The FEBS Journal 2006 273 1 159 169
78. Alexov E., Numerical calculations of the pH of maximal protein stability: the effect of the sequence composition and three-dimensional structure European Journal of Biochemistry 2004 271 1 173 185 (Pubitemid 38122176)
79. Fujiwara H., Tatsumi K. I., Tanaka S., Kimura M., Nose O., Amino N., A novel V59E missense mutation in the sodium iodide symporter gene in a family with iodide transport defect Thyroid 2000 10 6 471 474 (Pubitemid 30437147)
80. Dill K. A., Fiebig K. M., Chan H. S., Cooperativity in protein-folding kinetics Proceedings of the National Academy of Sciences of the United States of America 1993 90 5 1942 1946 (Pubitemid 23069973)
81. Dill K. A., Ozkan S. B., Weikl T. R., Chodera J. D., Voelz V. A., The protein folding problem: when will it be solved? Current Opinion in Structural Biology 2007 17 3 342 346 (Pubitemid 47021366)
82. Ye Y., Li Z., Godzik A., Modeling and analyzing three-dimensional structures of human disease proteins Pacific Symposium on Biocomputing 2006 439 450
83. Karchin R., Diekhans M., Kelly L., Thomas D. J., Pieper U., Eswar N., Haussler D., Sali A., LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources Bioinformatics 2005 21 12 2814 2820 (Pubitemid 40862277)
84. Wang Z., Moult J., SNPs, protein structure, and disease Human Mutation 2001 17 4 263 270 (Pubitemid 32268400)
85. Wang Z., Moult J., Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor V domain Proteins 2003 53 3 748 757 (Pubitemid 37352187)
86. Ramensky V., Bork P., Sunyaev S., Human non-synonymous SNPs: server and survey Nucleic Acids Research 2002 30 17 3894 3900 (Pubitemid 35012462)
87. Ode H., Matsuyama S., Hata M., Neya S., Kakizawa J., Sugiura W., Hoshino T., Computational characterization of structural role of the non-active site mutation M36I of human immunodeficiency virus type 1 protease Journal of Molecular Biology 2007 370 3 598 607 (Pubitemid 46901071)
88. Shirley B. A., Stanssens P., Hahn U., Pace C. N., Contribution of hydrogen bonding to the conformational stability of ribonuclease T1 Biochemistry 1992 31 3 725 732
89. Karplus M., Kuriyan J., Molecular dynamics and protein function Proceedings of the National Academy of Sciences of the United States of America 2005 102 19 6679 6685 (Pubitemid 40675376)
90. Young M. A., Gonfloni S., Superti-Furga G., Roux B., Kuriyan J., Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation Cell 2001 105 1 115 126 (Pubitemid 32323921)
91. Tang K. E. S., Dill K. A., Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability Journal of Biomolecular Structure and Dynamics 1998 16 2 397 411 (Pubitemid 28524884)
92. Song E. S., Daily A., Fried M. G., Juliano M. A., Juliano L., Hersh L. B., Mutation of active site residues of insulin-degrading enzyme alters allosteric interactions The Journal of Biological Chemistry 2005 280 18 17701 17706 (Pubitemid 41389007)
93. Valerio M., Colosimo A., Conti F., Giuliani A., Grottesi A., Manetti C., Zbilut J. P., Early events in protein aggregation: molecular flexibility and hydrophobicity/charge interaction in amyloid peptides as studied by molecular dynamics simulations Proteins 2005 58 1 110 118 (Pubitemid 39665621)
94. Board P. G., Pierce K., Coggan M., Expression of functional coagulation factor XIII in Escherichia coli Thrombosis and Haemostasis 1990 63 2 235 240 (Pubitemid 20128188)
95. Ozbabacan S. E. A., Gursoy A., Keskin O., Nussinov R., Conformational ensembles, signal transduction and residue hot spots: application to drug discovery Current Opinion in Drug Discovery and Development 2010 13 5 527 537
96. Dixit A., Torkamani A., Schork N. J., Verkhivker G., Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability Biophysical Journal 2009 96 3 858 874
97. Jones R., Ruas M., Gregory F., Moulin S., Delia D., Manoukian S., Rowe J., Brookes S., Peters G., A CDKN2A mutation in familial melanoma that abrogates binding of p16 INK4a to CDK4 but not CDK6 Cancer Research 2007 67 19 9134 9141 (Pubitemid 47535899)
98. Rignall T. R., Baker J. O., McCarter S. L., Adney W. S., Vinzant T. B., Decker S. R., Himmel M. E., Effect of single active-site cleft mutation on product specificity in a thermostable bacterial cellulase Applied Biochemistry and Biotechnology A 2002 98-100 383 394 (Pubitemid 34460647)
99. van Wijk R., Rijksen G., Huizinga E. G., Nieuwenhuis H. K., van Solinge W. W., HK Utrecht: missense mutation in the active site of human hexokinase associated with hexokinase deficiency and severe nonspherocytic hemolytic anemia Blood 2003 101 1 345 347 (Pubitemid 36025929)
100. Hardt M., Laine R. A., Mutation of active site residues in the chitin-binding domain ChBD ChiA1 from chitinase A1 of Bacillus circulans alters substrate specificity: use of a green fluorescent protein binding assay Archives of Biochemistry and Biophysics 2004 426 2 286 297 (Pubitemid 38680626)
101. Ortiz M. A., Light J., Maki R. A., Assa-Munt N., Mutation analysis of the pip interaction domain reveals critical residues for protein-protein interactions Proceedings of the National Academy of Sciences of the United States of America 1999 96 6 2740 2745 (Pubitemid 29148788)
102. Kim E., Hyrc K. L., Speck J., Salles F. T., Lundberg Y. W., Goldberg M. P., Kachar B., Warchol M. E., Ornitz D. M., Missense mutations in Otopetrin 1 affect subcellular localization and inhibition of purinergic signaling in vestibular supporting cells Molecular and Cellular Neuroscience 2011 46 3 655 661
103. Castella M., Pujol R., Callen E., Trujillo J. P., Casado J. A., Gille H., Lach F. P., Auerbach A. D., Schindler D., Benitez J., Porto B., Ferro T., Arturo M., Sevilla J., Madero L., Cela E., Belendez C., de Heredia C. D., Olive T., de Toledo J. S., Badell I., Torrent M., Estella J., Dasi A., Rodriguez-Villa A., Gemez P., Barbot J., Tapia M., Molines A., Figuera A., Bueren J. A., Surralles J., Origin, functional role, and clinical impact of fanconi anemia fanca mutations Blood 2011 117 14 3759 3769
104. Boulling A., le Marechal C., Trouve P., Raguenes O., Chen J. M., Ferec C., Functional analysis of pancreatitis-associated missense mutations in the pancreatic secretory trypsin inhibitor (SPINK1) gene European Journal of Human Genetics 2007 15 9 936 942 (Pubitemid 47308469)
105. Niel-Butschi F., Kantelip B., Iwaszkiewicz J., Zoete V., Boimard M., Delpech M., Bourges J. L., Renard G., D'Hermies F., Pisella P. J., Hamel C., Delbosc B., Valleix S., Genotype-phenotype correlations of TGFBI p.Leu509Pro, p.Leu509Arg, p.Val613Gly, and the allelic association of p.Met502Val-p.Arg555Gln mutations Molecular Vision 2011 17 1192 11202
106. Henriques B. J., Bross P., Gomes C. M., Mutational hotspots in electron transfer flavoprotein underlie defective folding and function in multiple acyl-CoA dehydrogenase deficiency Biochimica et Biophysica Acta 2010 1802 11 1070 1077
107. Khan S., Vihinen M., Performance of protein stability predictors Human Mutation 2010 31 6 675 684
108. Battiti R., Using mutual information for selecting features in supervised neural net learning IEEE Transactions on Neural Networks 1994 5 4 537 550
109. Karchin R., Kelly L., Sali A., Improving functional annotation of non-synonomous SNPs with information theory Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 397 408
110. Chasman D., Adams R. M., Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation Journal of Molecular Biology 2001 307 2 683 706 (Pubitemid 33027685)
111. Yue P., Moult J., Identification and analysis of deleterious human SNPs Journal of Molecular Biology 2006 356 5 1263 1274 (Pubitemid 43199928)
112. Yin S., Ding F., Dokholyan N. V., Eris: an automated estimator of protein stability Nature Methods 2007 4 6 466 467 (Pubitemid 46852064)
113. Cai J., Cai L. Q., Hong Y., Zhu Y. S., Functional characterisation of a natural androgen receptor missense mutation (N771H) causing human androgen insensitivity syndrome. submitted to Andrologia
114. Hunt D. M., Saldanha J. W., Brennan J. F., Benjamin P., Strom M., Cole J. A., Spreadbury C. L., Buxton R. S., Single nucleotide polymorphisms that cause structural changes in the cyclic AMP receptor protein transcriptional regulator of the tuberculosis vaccine strain Mycobacterium bovis BCG alter global gene expression without attenuating growth Infection and Immunity 2008 76 5 2227 2234 (Pubitemid 351656159)
115. Nicolao P., Carella M., Giometto B., Tavolato B., Cattin R., Giovannucci-Uzielli M. L., Vacca M., Regione F. D., Piva S., Bortoluzzi S., Gasparini P., Missense polymorphism in the human carboxypeptidase E gene alters enzymatic activity Human Mutation 2001 18 2 120 131 (Pubitemid 32726958)
116. Kollman P. A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D. A., Cheatham T. E. III, Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Accounts of Chemical Research 2000 33 12 889 897 (Pubitemid 32056774)
117. Cavallo A., Martin A. C. R., Mapping SNPs to protein sequence and structure data Bioinformatics 2005 21 8 1443 1450 (Pubitemid 40542699)
118. Ng P. C., Henikoff S., SIFT: predicting amino acid changes that affect protein function Nucleic Acids Research 2003 31 13 3812 3814 (Pubitemid 37442253)
119. Bao L., Cui Y., Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information Bioinformatics 2005 21 10 2185 2190 (Pubitemid 40731569)
120. Saunders C. T., Baker D., Evaluation of structural and evolutionary contributions to deleterious mutation prediction Journal of Molecular Biology 2002 322 4 891 901
121. Sunyaev S., Ramensky V., Bork P., Towards a structural basis of human non-synonymous single nucleotide polymorphisms Trends in Genetics 2000 16 5 198 200 (Pubitemid 30216541)
122. Sunyaev S. R., Lathe W. C. III, Ramensky V. E., Bork P., SNP frequencies in human genes: an excess of rare alleles and differing modes of selection Trends in Genetics 2000 16 8 335 337 (Pubitemid 30628833)
123. Sunyaev S., Ramensky V., Koch I., Lathe W. III, Kondrashov A. S., Bork P., Prediction of deleterious human alleles Human Molecular Genetics 2001 10 6 591 597 (Pubitemid 32229363)
124. Dimmic M. W., Sunyaev S., Bustamante C. D., Inferring SNP function using evolutionary, structural, and computational methods Pacific Symposium on Biocomputing 2005 382 384
125. Landgraf R., Xenarios I., Eisenberg D., Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins Journal of Molecular Biology 2001 307 5 1487 1502 (Pubitemid 33027653)
126. Lichtarge O., Sowa M. E., Evolutionary predictions of binding surfaces and interactions Current Opinion in Structural Biology 2002 12 1 21 27 (Pubitemid 34142716)
127. Innis C. A., Shi J., Blundell T. L., Evolutionary trace analysis of TGF- and related growth factors: implications for site-directed mutagenesis Protein Engineering 2000 13 12 839 847 (Pubitemid 32233943)
128. Lichtarge O., Bourne H. R., Cohen F. E., An evolutionary trace method defines binding surfaces common to protein families Journal of Molecular Biology 1996 257 2 342 358 (Pubitemid 26114038)
129. Porter C. T., Bartlett G. J., Thornton J. M., The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Research 2004 32 D129 D133
130. Chelliah V., Chen L., Blundell T. L., Lovell S. C., Distinguishing structural and functional restraints in evolution in order to identify interaction sites Journal of Molecular Biology 2004 342 5 1487 1504 (Pubitemid 39213963)
131. Pazos F., Sternberg M. J. E., Automated prediction of protein function and detection of functional sites from structure Proceedings of the National Academy of Sciences of the United States of America 2004 101 41 14754 14759 (Pubitemid 39410747)
132. Ding F., Dokholyan N. V., Emergence of protein fold families through rational design PLoS Computational Biology 2006 2 7 0725 0733 (Pubitemid 44147383)
133. Yin S., Ding F., Dokholyan N. V., Modeling backbone flexibility improves protein stability estimation Structure 2007 15 12 1567 1576 (Pubitemid 350213412)
134. Capriotti E., Fariselli P., Rossi I., Casadio R., A three-state prediction of single point mutations on protein stability changes BMC Bioinformatics 2008 9 supplement 2, article S6
135. Cheng J. L., Randall A., Baldi P., Prediction of protein stability changes for single-site mutations using support vector machines Proteins 2006 62 4 1125 1132 (Pubitemid 43364175)
136. Alva V., Syamala Devi D. P., Sowdhamini R., COILCHECK: an interactive server for the analysis of interface regions in coiled coils Protein and Peptide Letters 2008 15 1 33 38 (Pubitemid 351206473)
137. Kruger D. M., Gohlke H., DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions Nucleic Acids Research 2010 38 supplement 2 W480 W486
138. Yue P., Melamud E., Moult J., SNPs3D: candidate gene and SNP selection for association studies BMC Bioinformatics 2006 7, article no. 166
139. de Baets G., van Durme J., Reumers J., Maurer-Stroh S., Vanhee P., Dopazo J., Schymkowitz J., Rousseau F., Snpeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants Nucleic Acids Research 2012 40 D935 D939. submitted to Nucleic Acids Research
140. Fernandez-Escamilla A. M., Rousseau F., Schymkowitz J., Serrano L., Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins Nature Biotechnology 2004 22 10 1302 1306 (Pubitemid 39336784)
141. Maurer-Stroh S., Debulpaep M., Kuemmerer N., de la Paz M. L., Martins I. C., Reumers J., Morris K. L., Copland A., Serpell L., Serrano L., Schymkowitz J. W. H., Rousseau F., Exploring the sequence determinants of amyloid structure using position-specific scoring matrices Nature Methods 2010 7 3 237 242
142. van Durme J., Maurer-Stroh S., Gallardo R., Wilkinson H., Rousseau F., Schymkowitz J., Accurate prediction of DnaK-peptide binding via homology modelling and experimental data PLoS Computational Biology 2009 5 8
143. Kumar P., Henikoff S., Ng P. C., Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm Nature Protocols 2009 4 7 1073 1082
144. Adzhubei I. A., Schmidt S., Peshkin L., Ramensky V. E., Gerasimova A., Bork P., Kondrashov A. S., Sunyaev S. R., A method and server for predicting damaging missense mutations Nature Methods 2010 7 4 248 249
145. Tian J., Wu N., Guo X., Guo J., Zhang J., Fan Y., Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines BMC Bioinformatics 2007 8, article 450
146. Uzun A., Leslin C. M., Abyzov A., Ilyin V., Structure SNP (StSNP): a web
147. Masso M., Vaisman I. I., Knowledge-based computational mutagenesis for predicting the disease potential of human non-synonymous single nucleotide polymorphisms Journal of Theoretical Biology 2010 266 4 560 568
148. Brooks B. R., Brooks C. L. III, Mackerell A. D. Jr., Nilsson L., Petrella R. J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A. R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R. W., Post C. B., Pu J. Z., Schaefer M., Tidor B., Venable R. M., Woodcock H. L., Wu X., Yang W., York D. M., Karplus M., CHARMM: the biomolecular simulation program Journal of Computational Chemistry 2009 30 10 1545 1614
149. Cason A. L., Ikeguchi Y., Skinner C., Wood T. C., Holden K. R., Lubs H. A., Martinez F., Simensen R. J., Stevenson R. E., Pegg A. E., Schwartz C. E., X-linked spermine synthase gene (SMS) defect: the first polyamine deficiency syndrome European Journal of Human Genetics 2003 11 12 937 944 (Pubitemid 38072159)
150. de Alencastro G., McCloskey D. E., Kliemann S. E., Maranduba C. M. C., Pegg A. E., Wang X., Bertola D. R., Schwartz C. E., Passos-Bueno M. R., Sertie A. L., New SMS mutation leads to a striking reduction in spermine synthase protein function and a severe form of Snyder-Robinson X-linked recessive mental retardation syndrome Journal of Medical Genetics 2008 45 8 539 543
151. Becerra-Solano L. E., Butler J., Castaneda-Cisneros G., Mccloskey D. E., Wang X., Pegg A. E., Schwartz C. E., Sanchez-Corona J., Garcia-Ortiz J. E., A missense mutation, p.V132G, in the X-linked spermine synthase gene (SMS) causes Snyder-Robinson syndrome American Journal of Medical Genetics A 2009 149 3 328 335
152. Gerner E. W., Meyskens F. L. Jr., Polyamines and cancer: old molecules, new understanding Nature Reviews Cancer 2004 4 10 781 792 (Pubitemid 39331150)
153. Ikeguchi Y., Bewley M. C., Pegg A. E., Aminopropyltransferases: function, structure and genetics Journal of Biochemistry 2006 139 1 1 9 (Pubitemid 43258840)
154. Pegg A. E., Mammalian polyamine metabolism and function IUBMB Life 2009 61 9 880 894
155. Geerts D., Koster J., Albert D., Koomoa D. L. T., Feith D. J., Pegg A. E., Volckmann R., Caron H., Versteeg R., Bachmann A. S., The polyamine metabolism genes ornithine decarboxylase and antizyme 2 predict aggressive behavior in neuroblastomas with and without MYCN amplification International Journal of Cancer 2010 126 9 2012 2024
156. Wu H., Min J., Zeng H., McCloskey D. E., Ikeguchi Y., Loppnau P., Michael A. J., Pegg A. E., Plotnikov A. N., Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism The Journal of Biological Chemistry 2008 283 23 16135 16146
157. Xiang Z., Honig B., Extending the accuracy limits of prediction for side-chain conformations Journal of Molecular Biology 2001 311 2 421 430 (Pubitemid 32744551)
158. Ponder J. W., Tinker-Software Tools for Molecular Design 1999
159. Rajendran V., Purohit R., Sethumadhavan R., In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein. submitted to Amino Acids
160. van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A. E., Berendsen H. J. C., GROMACS: fast, flexible, and free Journal of Computational Chemistry 2005 26 16 1701 1718 (Pubitemid 43076182)
161. Minutolo C., Nadra A. D., Fernandez C., Taboas M., Buzzalino N., Casali B., Belli S., Charreau E. H., Alba L., Dain L., Structure-based analysis of five novel disease-causing mutations in 21-hydroxylase-deficient patients PLoS One 2011 6 1
162. Tan Y., Luo R., Structural and functional implications of p53 missense cancer mutations PMC Biophysics 2009 2 1, article 5
163. Lee W. H., Raas-Rotschild A., Miteva M. A., Bolasco G., Rein A., Gillis D., Vidaud D., Vidaud M., Villoutreix B. O., Parfait B., Noonan syndrome type I with PTPN11 3 bp deletion: structure-function implications Proteins 2005 58 1 7 13 (Pubitemid 39665611)
164. Abagyan R., Totrov M., Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins Journal of Molecular Biology 1994 235 3 983 1002 (Pubitemid 24047836)
165. Rocchia W., Alexov E., Honig B., Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions Journal of Physical Chemistry B 2001 105 28 6507 6514 (Pubitemid 35339019)
166. Alexov E. G., Gunner M. R., Calculated protein and proton motions coupled to electron transfer: electron transfer from Q A-to Q B in bacterial photosynthetic reaction centers Biochemistry 1999 38 26 8253 8270
167. Georgescu R. E., Alexov E. G., Gunner M. R., Combining conformational flexibility and continuum electrostatics for calculating PK a s in proteins Biophysical Journal 2002 83 4 1731 1748
168. Song Y., Mao J., Gunner M. R., MCCE2: improving protein PK a calculations with extensive side chain rotamer sampling Journal of Computational Chemistry 2009 30 14 2231 2247
169. Tynan-Connolly B. M., Nielsen J. E., pKD: re-designing protein PK a values Nucleic Acids Research 2006 34 W48 W51
170. Wei Q., Wang L., Wang Q., Kruger W. D., Dunbrack R. L. Jr., Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase Proteins 2010 78 9 2058 2074
171. Rajasekaran R., Sethumadhavan R., Exploring the cause of drug resistance by the detrimental missense mutations in KIT receptor: computational approach Amino Acids 2010 39 3 651 660
172. Abdur Rauf S. M., Ismael M., Sahu K. K., Suzuki A., Sahnoun R., Koyama M., Tsuboi H., Hatakeyama N., Endou A., Takaba H., del Carpio C. A., Kubo M., Miyamoto A., A graph theoretical approach to the effect of mutation on the flexibility of the DNA binding domain of p53 protein Chemical Papers 2009 63 6 654 661
173. Cheng T. M. K., Lu Y. E., Vendruscolo M., Lio P., Blundell T. L., Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms PLoS Computational Biology 2008 4 7
174. Danielian S., El-Hakeh J., Basilico G., Oleastro M., Rosenzweig S., Feldman G., Berozdnik L., Galicchio M., Gallardo A., Giraudi V., Liberatore D., Rivas E. M., Zelazko M., Bruton tyrosine kinase gene mutations in Argentina Human Mutation 2003 21 4 451
175. Iqbal H., Mir A., Faryal R., Molecular modeling of mutant kinase domain of Btk, a Tec family member, for structure prediction African Journal of Biotechnology 2011 10 17 3274 3289
176. Leandro J., Simonsen N., Saraste J., Leandro P., Flatmark T., Phenylketonuria as a protein misfolding disease: the mutation pG46S in phenylalanine hydroxylase promotes self-association and fibril formation Biochimica et Biophysica Acta 2011 1812 1 106 120
177. Yang Y., Zhou Y., Specific interactions for ab initio folding of protein terminal regions with secondary structures Proteins 2008 72 2 793 803 (Pubitemid 351928531)
178. Yang Y., Zhou Y., Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions Protein Science 2008 17 7 1212 1219 (Pubitemid 351930918)
179. Dehouck Y., Grosfils A., Folch B., Gilis D., Bogaerts P., Rooman M., Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 Bioinformatics 2009 25 19 2537 2543
180. Dehouck Y., Kwasigroch J. M., Gilis D., Rooman M., PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality BMC Bioinformatics 2011 12, article 151
181. Parthiban V., Gromiha M. M., Schomburg D., CUPSAT: prediction of protein stability upon point mutations Nucleic Acids Research 2006 34 W239 W242
182. Parthiban V., Gromiha M. M., Hoppe C., Schomburg D., Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility Proteins 2007 66 1 41 52 (Pubitemid 44955977)
183. Parthiban V., Gromiha M. M., Abhinandan M., Schomburg D., Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development BMC Structural Biology 2007 7, article 54
184. Wainreb G., Wolf L., Ashkenazy H., Dehouck Y., Ben-Tal N., Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site Bioinformatics 2011 27 23 3286 3292