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2001
Mas JM, Aloy P, Marti-Renom MA, et al. Classification of protein disulphide-bridge topologies. J Comput Aided Mol Des. 2001;15:477-87. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11394740.
Marti-Renom MA, Ilyin VA, Sali A. DBAli: a database of protein structure alignments. Bioinformatics. 2001;17:746-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11524379.
Eyrich VA, Marti-Renom MA, Przybylski D, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001;17:1242-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240.
2002
Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002;10:435-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12005441.
Iverson GM, Reddel S, Victoria EJ, et al. Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol. 2002;169:7097-103. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12471146.
2003
Koh IY, Eyrich VA, Marti-Renom MA, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003;31:3311-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003;19:165-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12499313.
Eswar N, John B, Mirkovic N, et al. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003;31:3375-80. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824331.
2004
Marti-Renom MA, Madhusudhan MS, Sali A. Alignment of protein sequences by their profiles. Protein Sci. 2004;13:1071-87. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15044736.
Pieper U, Eswar N, Braberg H, et al. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004;32:D217-22. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14681398.
Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res. 2004;64:3790-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15172985.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16170324.
Espadaler J, Aragues R, Eswar N, et al. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A. 2005;102:7151-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15883372.
2006
Melo F, Marti-Renom MA. Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Proteins. 2006;63:986-95. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16506243.
Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics. 2006;Chapter 5:Unit 5 6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18428767.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16751606.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16963645.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16381869.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16490207.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16423846.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17570147.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17941705.
Marti-Renom MA, Pieper U, Madhusudhan MS, et al. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007;35:W393-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478513.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17884042.
2008
Capriotti E, Marti-Renom MA. Assessment of protein structure predictions. In: Computational Structural Biology. Computational Structural Biology. New Jersey, USA: World Scientific Publishing Company; 2008. Available at: http://www.amazon.com/dp/9812778772/.