Premium
Cover Image, Volume 36, Issue 13
Publication year - 2015
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Reports
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23924
Subject(s) - dipeptide , computer science , cover (algebra) , dihydrofolate reductase , dihedral angle , graph , information retrieval , algorithm , computer graphics (images) , combinatorics , artificial intelligence , hydrogen bond , crystallography , chemistry , theoretical computer science , peptide , mathematics , molecule , enzyme , mechanical engineering , engineering , biochemistry , organic chemistry
On page 996 (DOI: 10.1002/jcc.23899 ), Elmar Krieger and Gert Vriend describe a collection of algorithms to accelerate molecular dynamics simulations. The validation of the protocol includes simulations of the enzyme dihydrofolate reductase (shown at the back) and a capped alanine dipeptide (shown at the front). The phi/psi dihedral angle distribution extracted from the latter simulation is depicted as a free energy landscape in shades of blue. One of the acceleration methods involves the LINCS algorithm, tuned to constrain not only bonds but also selected angles formed by hydrogen atoms. These constraints are shown in bright orange for the alanine dipeptide, and for a larger peptide with sequence AIAFAWARATA in the middle.