References

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J.Mol.Biol. 215(3):403-410.

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res 28(1):235-42.

Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I and others. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31(1):365-70.

Cortes C, Vapnik V. 1995. Support vector networks. Machine Learning 20:273-197.

Davis FP, Sali A. 2005. PIBASE: a comprehensive database of structurally defined protein domain interfaces. Bioinformatics.

Eddy SR. 1996. Hidden Markov models. Curr.Opin.Struct.Biol. 6(3):361-365.

Eigenbrot C, Kossiakoff AA. 1992. Structural consequences of mutation. Curr Opin Biotechnol 3(4):333-7.

Eswar N, John B, Mirkovic N, Fiser A, Ilyin V, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B and others. 2003. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 31:3375-3380.

Feyfant E, Fiser A, Sali A. 2004. Modeling mutations in protein structures. In preparation.

Flanagan JU, Rossjohn J, Parker MW, Board PG, Chelvanayagam G. 1998. A homology model for the human theta-class glutathione transferase T1-1. Proteins 33(3):444-54.

Frayling IM, Beck NE, Ilyas M, Dove-Edwin I, Goodman P, Pack K, Bell JA, Williams CB, Hodgson SV, Thomas HJ and others. 1998. The APC variants I1307K and E1317Q are associated with colorectal tumors, but not always with a family history. Proc Natl Acad Sci U S A 95(18):10722-7.

Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P and others. 2004. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res 14(10B):2121-7.

Huang CC, Couch GS, Pettersen EF, Ferrin TE. 1996. Chimera: an extensible molecular modeling application constructed using standard components. Pac.Symp.Biocomput. 1:724.

Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577-637.

Karchin R, Kelly L, Sali A. 2005. Improving functional annotation of non-synonymous SNPs with information theory. Pac.Symp.Biocomput.

Karplus K, Barrett C, Hughey R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics. 14(10):846-856.

Kent WJ. 2002. BLAT--the BLAST-like alignment tool. Genome Res 12(4):656-64.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res. 12(6):996-1006.

Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology: applications to protein modeling. J.Mol.Biol. 235:1501-1531.

Lamlum H, Al Tassan N, Jaeger E, Frayling I, Sieber O, Reza FB, Eckert M, Rowan A, Barclay E, Atkin W and others. 2000. Germline APC variants in patients with multiple colorectal adenomas, with evidence for the particular importance of E1317Q. Hum Mol Genet 9(15):2215-21.

Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM. 1997. PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci 22(12):488-90.

Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. 1998a. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 33(1):1-17.

Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. 1998b. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins 33(1):18-29.

Maglott DR, Katz KS, Sicotte H, Pruitt KD. 2000. NCBI's LocusLink and RefSeq. Nucleic Acids Res 28(1):126-8.

Mangalam H. 2002. The Bio* toolkits--a brief overview. Brief Bioinform 3(3):296-302.

McKusick V. 2000. Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD).

Melo F, Sanchez R, Sali A. 2002. Statistical potentials for fold assessment. Protein Sci. 11(2):430-448.

Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247(4):536-40.

NCBI. 2004. dbSNP database, build 120.

Nijbroek G, Sood S, McIntosh I, Francomano CA, Bull E, Pereira L, Ramirez F, Pyeritz RE, Dietz HC. 1995. Fifteen novel FBN1 mutations causing Marfan syndrome detected by heteroduplex analysis of genomic amplicons. Am J Hum Genet 57(1):8-21.

Ory PA, Clark MR, Kwoh EE, Clarkson SB, Goldstein IM. 1989. Sequences of complementary DNAs that encode the NA1 and NA2 forms of Fc receptor III on human neutrophils. J Clin Invest 84(5):1688-91.

Pianezza ML, Sellers EM, Tyndale RF. 1998. Nicotine metabolism defect reduces smoking. Nature 393(6687):750.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis F, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A and others. 2004. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32:D217-D222.

Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30(17):3894-3900.

Rossjohn J, McKinstry WJ, Oakley AJ, Verger D, Flanagan J, Chelvanayagam G, Tan KL, Board PG, Parker MW. 1998. Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site. Structure 6(3):309-22.

Rost B, Sander C. 1994. Conservation and prediction of solvent accessibility in protein families. Proteins 20(3):216-26.

Sali A, Blundell TL. 1993. Comparative protein modelling by satisfaction of spatial restraints. J.Mol.Biol. 234(3):779-815.

Sanchez R, Sali A. 1998. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc.Natl.Acad.Sci.U.S.A 95(23):13597-13602.

Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF. 1999. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 15(12):1000-1011.

Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29(1):308-311.

Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. 2003. Structural location of disease-associated single-nucleotide polymorphisms. J.Mol.Biol. 327(5):1021-1030.

Stuart AC, Ilyin VA, Sali A. 2002. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18(1):200-201.

Sunyaev S, Ramensky V, Koch I, Lathe W, III, Kondrashov AS, Bork P. 2001. Prediction of deleterious human alleles. Hum.Mol.Genet. 10(6):591-597.

van Kuilenburg AB, Dobritzsch D, Meinsma R, Haasjes J, Waterham HR, Nowaczyk MJ, Maropoulos GD, Hein G, Kalhoff H, Kirk JM and others. 2002. Novel disease-causing mutations in the dihydropyrimidine dehydrogenase gene interpreted by analysis of the three-dimensional protein structure. Biochem J 364(Pt 1):157-63.

Vapnik V. 1995. The Nature of Statistical Learning Theory. New York: Springer-Verlag.

Vreken P, Van Kuilenburg AB, Meinsma R, van Gennip AH. 1997. Dihydropyrimidine dehydrogenase (DPD) deficiency: identification and expression of missense mutations C29R, R886H and R235W. Hum Genet 101(3):333-8.

Wang Z, Moult J. 2001. SNPs, protein structure, and disease. Hum.Mutat. 17(4):263-270.

Yamano S, Tatsuno J, Gonzalez FJ. 1990. The CYP2A3 gene product catalyzes coumarin 7-hydroxylation in human liver microsomes. Biochemistry 29(5):1322-9.

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. 2004. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat 23(5):464-70.