Protein structure modeling with MODELLER.

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

[1]  B. Rost.  Twilight zone of protein sequence alignments. , 1999, Protein engineering.

[2]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[3]  Qing Zhang,et al.  The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema , 2004, Nucleic Acids Res..

[4]  Frank Alber,et al.  Integrating diverse data for structure determination of macromolecular assemblies. , 2008, Annual review of biochemistry.

[5]  A. Sali,et al.  Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Marc A. Martí-Renom,et al.  MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..

[7]  Roland L. Dunbrack.  Sequence comparison and protein structure prediction. , 2006, Current opinion in structural biology.

[8]  A. Sali,et al.  A composite score for predicting errors in protein structure models , 2006, Protein science : a publication of the Protein Society.

[9]  Baldomero Oliva,et al.  A supersecondary structure library and search algorithm for modeling loops in protein structures , 2006, Nucleic acids research.

[10]  Narayanan Eswar,et al.  Alignment of multiple protein structures based on sequence and structure features. , 2009, Protein engineering, design & selection : PEDS.

[11]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[12]  John P. Overington,et al.  Derivation of rules for comparative protein modeling from a database of protein structure alignments , 1994, Protein science : a publication of the Protein Society.

[13]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[14]  Yang Zhang.  Progress and challenges in protein structure prediction. , 2008, Current opinion in structural biology.

[15]  Liam J. McGuffin,et al.  Improvement of the GenTHREADER Method for Genomic Fold Recognition , 2003, Bioinform..

[16]  A. Fiser,et al.  Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  T L Blundell,et al.  An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. , 1993, Protein engineering.

[18]  A. Sali,et al.  Comparative protein structure modeling by iterative alignment, model building and model assessment. , 2003, Nucleic Acids Research.

[19]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[20]  Andrej Sali,et al.  Variable gap penalty for protein sequence-structure alignment. , 2006, Protein engineering, design & selection : PEDS.

[21]  Roland L Dunbrack,et al.  Outcome of a workshop on applications of protein models in biomedical research. , 2009, Structure.

[22]  A. Sali,et al.  Statistical potentials for fold assessment , 2009 .

[23]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[24]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[25]  M. Karplus,et al.  PDB-based protein loop prediction: parameters for selection and methods for optimization. , 1997, Journal of molecular biology.

[26]  Chaok Seok,et al.  A kinematic view of loop closure , 2004, J. Comput. Chem..

[27]  A. C. May,et al.  Percent sequence identity; the need to be explicit. , 2004, Structure.

[28]  T L Blundell,et al.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.

[29]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[30]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[31]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[32]  A. Sali,et al.  The molecular sociology of the cell , 2007, Nature.

[33]  K. Ginalski.  Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.

[34]  R Sánchez,et al.  Evaluation of comparative protein structure modeling by MODELLER‐3 , 1997, Proteins.

[35]  Hongyi Zhou,et al.  Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments , 2004, Proteins.

[36]  Z. Xiang,et al.  Advances in homology protein structure modeling. , 2006, Current protein & peptide science.

[37]  Richard Bonneau,et al.  Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.

[38]  David Baker,et al.  Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.

[39]  Dima Kozakov,et al.  Convergence and combination of methods in protein-protein docking. , 2009, Current opinion in structural biology.

[40]  K. Karplus,et al.  Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry , 2003, Proteins.

[41]  R Sánchez,et al.  Advances in comparative protein-structure modelling. , 1997, Current opinion in structural biology.

[42]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[43]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[44]  R. Friesner,et al.  Long loop prediction using the protein local optimization program , 2006, Proteins.

[45]  W. Pearson.  Empirical statistical estimates for sequence similarity searches. , 1998, Journal of molecular biology.

[46]  A. Sali,et al.  How well can the accuracy of comparative protein structure models be predicted? , 2008, Protein science : a publication of the Protein Society.

[47]  B. Honig,et al.  A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.

[48]  A. Sali,et al.  Alignment of protein sequences by their profiles , 2004, Protein science : a publication of the Protein Society.

[49]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[50]  J. Skolnick,et al.  Automated structure prediction of weakly homologous proteins on a genomic scale. , 2004, Proceedings of the National Academy of Sciences of the United States of America.