Molecular dynamics simulation of peptide folding

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Abstract

The simulation of peptide folding with atomic resolution has evolved remarkably during the last 7 years, i.e., from absolute skepticism on the capability of classical molecular dynamics (MD) methodology to reproduce complex biological phenomena such as the folding of even simple oligopeptides (6-15 residues) to the seemingly realistic representation of the thermodynamics and kinetics of folding of a rapidly increasing number of polypeptides (over 20 residues). Four factors permitted this rapid progress: the breakthrough of a second generation of force fields, a rapid and steady increase of (commodity) computer performance, a move from local computational resources to large distributed clusters and, last but not less important, a decision of particular groups to spend a large computational effort on projects that most other groups trusted unrealizable at the time. The present account goes over some aspects of peptide folding and its simulation with MD techniques while sweeping through the simulation landmarks of the last 7 years and conjecturing on the future.
Original languageEnglish
Pages (from-to)297-306
JournalTheoretical Chemistry Accounts
Volume116
DOIs
Publication statusPublished - 1 Aug 2006

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