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80. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK-a program to check the stereochemical quality of prote<strong>in</strong> structures. J.<br />

Appl. Cryst 26: 283–291.<br />

81. Wesson L, Eisenberg D (1992) Atomic solvation parameters applied to molecular dynamics of prote<strong>in</strong>s <strong>in</strong> solution. Prote<strong>in</strong> Sci 1: 227-235.<br />

82. Bates PA, Sternberg MJ (1999) Model build<strong>in</strong>g by comparison at CASP3: us<strong>in</strong>g expert knowledge and computer automation. Prote<strong>in</strong>s Suppl 3: 47-54.<br />

83. Söd<strong>in</strong>g J (2005) Prote<strong>in</strong> homology detection by HMM-HMM comparison. Bio<strong>in</strong>formatics 21: 951-960.<br />

84. Kim DE, Chivian D, Baker D (2004) Prote<strong>in</strong> structure prediction and analysis us<strong>in</strong>g the Robetta server. Nucleic Acids Res 32: W526-531.<br />

85. Bowers PM, Strauss CE, Baker D (2000) De novo prote<strong>in</strong> structure determ<strong>in</strong>ation us<strong>in</strong>g sparse NMR data. J Biomol NMR 18: 311-318.<br />

86. Meiler J, Baker D (2003) Rapid prote<strong>in</strong> fold determ<strong>in</strong>ation us<strong>in</strong>g unassigned NMR data. Proc Natl Acad Sci U S A 100: 15404-15409.<br />

87. Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, et al. (2003) Automated prediction of CASP-5 structures us<strong>in</strong>g the Robetta server. Prote<strong>in</strong>s<br />

53 Suppl 6: 524-533.<br />

88. Ortiz AR, Strauss CE, Olmea O (2002) MAMMOTH (match<strong>in</strong>g molecular models obta<strong>in</strong>ed from theory): an automated method for model comparison.<br />

Prote<strong>in</strong> Sci 11: 2606-2621.<br />

89. Lambert C, Léonard N, De Bolle X, Depiereux E (2002) ESyPred3D: Prediction of prote<strong>in</strong>s 3D structures. Bio<strong>in</strong>formatics 18: 1250-1256.<br />

90. Nielsen M, Lundegaard C, Lund O, Petersen TN (2010) CPHmodels-3.0--remote homology model<strong>in</strong>g us<strong>in</strong>g structure-guided sequence profiles.<br />

Nucleic Acids Res 38: W576-581.<br />

91. Jayaram B, Dh<strong>in</strong>gra P, Lakhani B, Shekhar S (2012) Bhageerath-Target<strong>in</strong>g the near impossible: Push<strong>in</strong>g the frontiers of atomic models for prote<strong>in</strong><br />

tertiary structure prediction. J. Chem. Sci 124: 83–91.<br />

92. Narang P, Bhushan K, Bose S, Jayaram B (2006) Prote<strong>in</strong> structure evaluation us<strong>in</strong>g an all-atom energy based empirical scor<strong>in</strong>g function. J Biomol<br />

Struct Dyn 23: 385-406.<br />

93. Kuntal BK, Aparoy P, Reddanna P (2010) EasyModeller: A graphical <strong>in</strong>terface to MODELLER. BMC Res Notes 3: 226.<br />

94. Kurowski MA, Bujnicki JM (2003) GeneSilico prote<strong>in</strong> structure prediction meta-server. Nucleic Acids Res 31: 3305-3307.<br />

95. Kos<strong>in</strong>ski J, Cymerman IA, Feder M, Kurowski MA, Sas<strong>in</strong> JM, et al. (2003) A “FRankenste<strong>in</strong>’s monster” approach to comparative model<strong>in</strong>g: merg<strong>in</strong>g the<br />

f<strong>in</strong>est fragments of Fold-Recognition models and iterative model ref<strong>in</strong>ement aided by 3D structure evaluation. Prote<strong>in</strong>s 53: 369-379.<br />

96. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, et al. (2003) The InterPro Database, 2003 br<strong>in</strong>gs <strong>in</strong>creased coverage and new features.<br />

Nucleic Acids Res 31: 315-318.<br />

97. Jones DT (1999) Prote<strong>in</strong> secondary structure prediction based on position-specific scor<strong>in</strong>g matrices. J Mol Biol 292: 195-202.<br />

98. Karplus K, Karch<strong>in</strong> R, Barrett C, Tu S, Cl<strong>in</strong>e M, et al. (2001) What is the value added by human <strong>in</strong>tervention <strong>in</strong> prote<strong>in</strong> structure prediction? Prote<strong>in</strong>s<br />

Suppl 5: 86-91.<br />

99. Ouali M, K<strong>in</strong>g RD (2000) Cascaded multiple classifiers for secondary structure prediction. Prote<strong>in</strong> Sci 9: 1162-1176.<br />

100. Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of all-helical membrane prote<strong>in</strong> structure and topology.<br />

Bio<strong>chemistry</strong> 33: 3038-3049.<br />

101. Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predict<strong>in</strong>g transmembrane helices <strong>in</strong> prote<strong>in</strong> sequences. Proc Int Conf<br />

Intell Syst Mol Biol 6: 175-182.<br />

102. Hofmann K and Stoffel W (1993) TMbase—a database of membrane spann<strong>in</strong>g prote<strong>in</strong>s segments. Biol Chem Hoppe-Seyler 374, 166.<br />

103. Xu J, Li M, Kim D, Xu Y (2003) RAPTOR: optimal prote<strong>in</strong> thread<strong>in</strong>g by l<strong>in</strong>ear programm<strong>in</strong>g. J Bio<strong>in</strong>form Comput Biol 1: 95-117.<br />

104. Kelley LA, MacCallum RM, Sternberg MJ (2000) Enhanced genome annotation us<strong>in</strong>g structural profiles <strong>in</strong> the program 3D-PSSM. J Mol Biol 299: 499-520.<br />

105. Shi J, Blundell TL, Mizuguchi K (2001) FUGUE: sequence-structure homology recognition us<strong>in</strong>g environment-specific substitution tables and structuredependent<br />

gap penalties. J Mol Biol 310: 243-257.<br />

106. Jones DT (1999) GenTHREADER: an efficient and reliable prote<strong>in</strong> fold recognition method for genomic sequences. J Mol Biol 287: 797-815.<br />

107. Rychlewski L, Jaroszewski L, Li W, Godzik A (2000) Comparison of sequence profiles. Strategies for structural predictions us<strong>in</strong>g sequence <strong>in</strong>formation.<br />

Prote<strong>in</strong> Sci. 9: 232–241.<br />

108. Karplus K, Karch<strong>in</strong> R, Barrett C, Tu S, Cl<strong>in</strong>e M, et al. (2001) What is the value added by human <strong>in</strong>tervention <strong>in</strong> prote<strong>in</strong> structure prediction? Prote<strong>in</strong>s<br />

Suppl 5: 86-91.<br />

109. Fischer D (2000) Hybrid fold recognition: comb<strong>in</strong><strong>in</strong>g sequence derived properties with evolutionary <strong>in</strong>formation. Pac Symp Biocomput .<br />

110. Lundström J, Rychlewski L, Bujnicki J, Elofsson A (2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Prote<strong>in</strong><br />

Sci 10: 2354-2362.<br />

111. Dunbrack RL Jr (1999) Comparative model<strong>in</strong>g of CASP3 targets us<strong>in</strong>g PSI-BLAST and SCWRL. Prote<strong>in</strong>s Suppl 3: 81-87.<br />

112. Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of prote<strong>in</strong> models with three-dimensional profiles. Nature 356: 83-85.<br />

113. Combet C, Jambon M, Deléage G, Geourjon C (2002) Geno3D: automatic comparative molecular modell<strong>in</strong>g of prote<strong>in</strong>. Bio<strong>in</strong>formatics 18: 213-214.<br />

114. Lobley A, Sadowski MI, Jones DT (2009) pGenTHREADER and pDomTHREADER: new methods for improved prote<strong>in</strong> fold recognition and superfamily<br />

discrim<strong>in</strong>ation. Bio<strong>in</strong>formatics 25: 1761-1767.<br />

115. Jones DT (2007) Improv<strong>in</strong>g the accuracy of transmembrane prote<strong>in</strong> topology prediction us<strong>in</strong>g evolutionary <strong>in</strong>formation. Bio<strong>in</strong>formatics 23: 538-544.<br />

116. Nugent T, Jones DT (2009) Transmembrane prote<strong>in</strong> topology prediction us<strong>in</strong>g support vector mach<strong>in</strong>es. BMC Bio<strong>in</strong>formatics 10: 159.<br />

117. Sodhi JS, Bryson K, McGuff<strong>in</strong> LJ, Ward JJ, Wernisch L, et al. (2004) Predict<strong>in</strong>g metal-b<strong>in</strong>d<strong>in</strong>g site residues <strong>in</strong> low-resolution structural models. J Mol<br />

Biol 342: 307-320.<br />

118. Ward JJ, McGuff<strong>in</strong> LJ, Bryson K, Buxton BF, Jones DT (2004) The DISOPRED server for the prediction of prote<strong>in</strong> disorder. Bio<strong>in</strong>formatics 20: 2138-2139.<br />

119. Bryson K, Cozzetto D, Jones DT (2007) Computer-assisted prote<strong>in</strong> doma<strong>in</strong> boundary prediction us<strong>in</strong>g the DomPred server. Curr Prote<strong>in</strong> Pept Sci 8: 181-188.<br />

120. Lobley AE, Nugent T, Orengo CA, Jones DT (2008) FFPred: an <strong>in</strong>tegrated feature-based function prediction server for vertebrate proteomes. Nucleic<br />

Acids Res 36: W297-302.<br />

121. Buchan DW, Ward SM, Lobley AE, Nugent TC, Bryson K, et al. (2010) Prote<strong>in</strong> annotation and modell<strong>in</strong>g servers at University College London. Nucleic<br />

Acids Res 38: W563-568.<br />

122. Peng J, Xu J (2010) Low-homology prote<strong>in</strong> thread<strong>in</strong>g. Bio<strong>in</strong>formatics 26: i294-300.<br />

OMICS Group eBooks<br />

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