BioInfo bibliography

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2010
Capriotti E, Marti-Renom MA. "Quantifying the relationship between sequence and three-dimensional structure conservation in RNA." BMC bioinformatics. 2010;11(1):322. Abstract
2009
Orti L, Carbajo RJ, Pieper U, et al. "A kernel for the Tropical Disease Initiative." Nat Biotechnol. 2009;27:320-1. Download: PDF (935.08 KB)
Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. "ModLink+: Improving fold recognition by using protein-protein interactions." Bioinformatics. 2009. Abstract
Capriotti E, Marti-Renom MA. "SARA: a server for function annotation of RNA structures." Nucl. Acids Res.. 2009:gkp433. Abstract
Marti-Renom MA, Capriotti E, Shindyalov I, Bourne P. "Structural Comparison and Alignment.". In: Structural Bioinformatics. 2nd ed. New Jersey. USA: Wiley-Blackwell; 2009.
Orti L, Carbajo RJ, Pieper U, et al. "A kernel for open source drug discovery in tropical diseases." PLoS Negl Trop Dis. 2009;3:e418. Abstract
Pieper U, Eswar N, Webb BM, et al. "MODBASE, a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res. 2009;37:D347-54. Abstract
2008
Capriotti E, Marti-Renom MA. "Assessment of protein structure predictions.". In: Computational Structural Biology. New Jersey, USA: World Scientific Publishing Company; 2008.
Panjkovich A, Melo F, Marti-Renom MA. "Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs." Genome Biol. 2008;9:R68. Abstract
Espadaler J, Eswar N, Querol E, et al. "Prediction of enzyme function by combining sequence similarity and protein interactions." BMC Bioinformatics. 2008;9:249. Abstract
Capriotti E, Marti-Renom MA. "RNA structure alignment by a unit-vector approach." Bioinformatics. 2008;24:i112-8. Abstract
Capriotti E, Arbiza L, Casadio R, Dopazo J, Dopazo H, Marti-Renom MA. "Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans." Hum Mutat. 2008;29:198-204. Abstract
2007
Marti-Renom MA, Rossi A, Al-Shahrour F, et al. "The AnnoLite and AnnoLyze programs for comparative annotation of protein structures." BMC Bioinformatics. 2007;8 Suppl 4:S4. Abstract
Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. "Characterization of protein hubs by inferring interacting motifs from protein interactions." PLoS Comput Biol. 2007;3:1761-71. Abstract
Eswar N, Webb B, Marti-Renom MA, et al. "Comparative protein structure modeling using MODELLER." Curr Protoc Protein Sci. 2007;Chapter 2:Unit 2 9. Abstract
Marti-Renom MA, Pieper U, Madhusudhan MS, et al. "DBAli tools: mining the protein structure space." Nucleic Acids Res. 2007;35:W393-7. Abstract
Stanley WA, Fodor K, Marti-Renom MA, Schliebs W, Wilmanns M. "Protein translocation into peroxisomes by ring-shaped import receptors." FEBS Lett. 2007;581:4795-802. Abstract
2006
Melo F, Marti-Renom MA. "Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets." Proteins. 2006;63:986-95. Abstract
Eswar N, Webb B, Marti-Renom MA, et al. "Comparative protein structure modeling using Modeller." Curr Protoc Bioinformatics. 2006;Chapter 5:Unit 5 6. Abstract
Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. "A composite score for predicting errors in protein structure models." Protein Sci. 2006;15:1653-66. Abstract
Rossi A, Marti-Renom MA, Sali A. "Localization of binding sites in protein structures by optimization of a composite scoring function." Protein Sci. 2006;15:2366-80. Abstract
Pieper U, Eswar N, Davis FP, et al. "MODBASE: a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res. 2006;34:D291-5. Abstract
Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. "Refinement of protein structures by iterative comparative modeling and CryoEM density fitting." J Mol Biol. 2006;357:1655-68. Abstract
Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. "Variable gap penalty for protein sequence-structure alignment." Protein Eng Des Sel. 2006;19:129-33. Abstract
2005
McMahon SA, Miller JL, Lawton JA, et al. "The C-type lectin fold as an evolutionary solution for massive sequence variation." Nat Struct Mol Biol. 2005;12:886-92. Abstract