Computational Approaches in Peptide and Protein Design: An Overview

Gregory V. Nikiforovich, Garland R. Marshall

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

2 Scopus citations
Original languageEnglish
Title of host publicationPeptide and Protein Design for Biopharmaceutical Applications
PublisherJohn Wiley and Sons
Number of pages44
ISBN (Print)9780470319611
StatePublished - Sep 21 2009


  • 3D arrangement of functional groups of ligand and '3D pharmacophore'
  • CXCR4 G-protein-coupled receptor (GPCR) and cyclopentapeptide inhibitors
  • Cambridge Structural Database (CSD), Protein Data Bank (PDB) and Swiss-Prot/TrEMBL
  • Critical assessment of structure predictions (CASP)
  • Energy estimations based on GROMOS or OPLS-AA force fields
  • GROMOS and OPLS-AA maps
  • Modern peptide and protein drug design problems - structure-based and target-based design
  • Peptide and protein design computational approaches
  • QM/MM and polarizable force fields in peptide and protein design
  • Routine MM force fields - AMBER, OPLS, ECEPP

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