@article{a6bab05ab1c34dcebdccd599f2551569,
title = "Efficient conformational search method for peptides and proteins: Monte Carlo minimization with an adaptive bias",
abstract = "The energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM), which corresponds to the native structure, is a severe problem in global optimization. The commonly used Monte Carlo minimization (MCM) method is based on a random selection of torsional angle values. We suggest selecting these values with biased probabilities depending on the increased structure-energy correlations as the GEM is approached during the search. Our method applied to models of the 5-residue peptide Leu-enkephalin finds the GEM ∼2.7 faster than MCM.",
author = "Ozkan, {S. Banu} and Hagai Meirovitch",
note = "Funding Information: Abbreviations: ER, estrogen receptor; MAP, mitogen-activated protein; Src, steroid receptor-coactivator; Shc, Src-homology/collagen protein; ERK, extracellular regulated kinases; MEK, mitogen-activated/extracellular-signal regulated protein kinase; BDL, bile duct ligated; p, phosphorylated; PCNA, proliferating cellular nuclear antigen. From the 1Department of Clinical Medicine, Division of Gastroenterology, and 7Department of Human Anatomy, University of Rome, La Sapienza, Rome; 2Department of Gastroenterology, University of Ancona, Ancona; 3Unit for Metabolic Diseases, H. S. Raffaele and Department of Internal Medicine, University of Milan, Milan; 4Department of Experimental Medicine, Section of Human & Clinical Anatomy, State University of L{\textquoteright}Aquila, L{\textquoteright}Aquila, Italy; 5Department of Internal Medicine and Medical Physiology, Scott & White Hospital and Texas A&M University System Health Science Center, College of Medicine, Temple; and the 6Central Veterans Health Care, Temple, TX. Received January 14, 2002; accepted May 13, 2002. Supported by Ministero Istruzione Universit{\`a} e Ricerca (MIUR) grants to E.G. and P.O. (Biomedicina, Cluster 04, progetto no 5, Cofin 2000, and ex 60% funds), a grant awarded to G.A. from Scott & White Hospital and Texas A&M University, by a National Institutes of Health grant DK58411, and by a Veterans Affairs Merit Award to G.A. D.A. and A.F.A. are supported by an MIUR grant (40% funds; MM06215421/2). Address reprint requests to: Eugenio Gaudio, M.D., Department of Human Anatomy, via A. Borelli 50, 00161 Rome, Italy. E-mail: eugenio.gaudio@ uniroma1.it; fax: (39) 06-49918062. Copyright {\textcopyright} 2002 by the American Association for the Study of Liver Diseases. 0270-9139/02/3602-0006$35.00/0 doi:10.1053/jhep.2002.34741",
year = "2003",
month = aug,
day = "28",
doi = "10.1021/jp0346615",
language = "English (US)",
volume = "107",
pages = "9128--9131",
journal = "Journal of Physical Chemistry B",
issn = "1520-6106",
number = "34",
}