D. Zupanic et al., GLOBAL ENERGY MINIMIZATION OF SMALL MOLECULES COMBINING CONSTRAINT LOGIC PROGRAMMING AND MOLECULAR MECHANICS, Journal of chemical information and computer sciences, 37(6), 1997, pp. 966-970
Citations number
22
Categorie Soggetti
Information Science & Library Science","Computer Application, Chemistry & Engineering","Computer Science Interdisciplinary Applications",Chemistry,"Computer Science Information Systems
The paper presents an approach to molecular energy minimization using
Constraint Logic Programming (CLP) as a preprocessor to a molecular me
chanics minimization program such as CHARMM. The use of CLP enables th
e definition of simple constraints that sufficiently describe relation
s in a molecule, thus limiting the search space of the globally optima
l solution. The approach was used on the problem of minimizing the ene
rgy of the alanine dipeptide and N-methylalanylacetamide. An approxima
te 3-D structure produced by a CLP system was used as an initial struc
ture for the CHARMM program that considers all relations in such a str
ucture and performs energy optimization With this initial structure, c
omputed in about 1 min of CPU time, the optimal solution (global minim
um) was found in only a few seconds, while calculating the same soluti
on with CHARMM alone took 15 h. All calculation were performed on HP/7
35.