ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes

We present the first applications of an activated method in internal coordinate space for sampling all‐atom protein conformations, the activation–relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate‐based studies aimed at...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2006-06, Vol.63 (4), p.967-975
Main Authors: Yun, Mi-Ran, Lavery, R., Mousseau, N., Zakrzewska, K., Derreumaux, P.
Format: Article
Language:English
Subjects:
Alanine - chemistry
Alanine - metabolism
ARTIST
Biochemistry, Molecular Biology
Computational Biology - methods
Drug Design
Life Sciences
Models, Molecular
Peptides - chemistry
Peptides - metabolism
protein energy landscapes
Protein Folding
Protein Structure, Tertiary
Ribonuclease H - chemistry
Ribonuclease H - metabolism
Software
Thermodynamics
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Summary:We present the first applications of an activated method in internal coordinate space for sampling all‐atom protein conformations, the activation–relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate‐based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well‐defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer‐aided drug design to supramolecular assembly. Proteins 2006. © 2006 Wiley‐Liss, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/prot.20938