Protocol

Structural Proteomics

Volume 426 of the series Methods in Molecular Biology™ pp 145-159

Protein Structure Modeling with MODELLER

  • Narayanan EswarAffiliated withDepartments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco
  • , David EramianAffiliated withDepartments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco
  • , Ben WebbAffiliated withDepartments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco
  • , Min-Yi ShenAffiliated withDepartments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco
  • , Andrej SaliAffiliated withDepartments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco

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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 protcols has resulted in models of useful accuracy for domains in more than half of all known protein sequences.