Premium
Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics
Author(s) -
Corcho Francesc J.,
Canto Josep,
Perez Juan J.
Publication year - 2004
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20114
Subject(s) - molecular dynamics , simulated annealing , computational chemistry , annealing (glass) , chemistry , chemical physics , statistical physics , computer science , thermodynamics , physics , algorithm
The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former method, the peptide was studied in vacuo with a dielectric constant of 80, whereas using the latter study the peptide was studied in a box of TIP3P water molecules. Analysis of the results obtained using both methodologies was carried out using an in‐house methodology using a cluster analysis method based on information theory. Comparison of the two sampling methodologies and the different environment used in the calculations is also analyzed. Finally, the conformational motifs that are characteristic of substance P in a hydrophilic environment are presented and compared with the experimental results available in the literature. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1937–1952, 2004