{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T22:50:13Z","timestamp":1776811813079,"version":"3.51.2"},"reference-count":38,"publisher":"European Society of Computational Methods in Sciences and Engineering","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JCM"],"published-print":{"date-parts":[[2017,8,8]]},"DOI":"10.3233\/jcm-170735","type":"journal-article","created":{"date-parts":[[2017,6,21]],"date-time":"2017-06-21T08:10:19Z","timestamp":1498032619000},"page":"595-609","source":"Crossref","is-referenced-by-count":1,"title":["Exploring potential energy surfaces of biological molecules using a Multi-Niche Crowding genetic algorithm"],"prefix":"10.66113","volume":"17","author":[{"given":"Anouar","family":"El Guerdaoui","sequence":"first","affiliation":[{"name":"Equipe de Chimie Th\u00e9orique, Electrochimie et Environnement CT2E, Facult\u00e9 des Sciences, Universit\u00e9 Ibn Zohr, Agadir, Maroc"}]},{"given":"Rachida","family":"Tijar","sequence":"additional","affiliation":[{"name":"Equipe de Chimie Th\u00e9orique, Electrochimie et Environnement CT2E, Facult\u00e9 des Sciences, Universit\u00e9 Ibn Zohr, Agadir, Maroc"}]},{"given":"Brahim","family":"El Merbouh","sequence":"additional","affiliation":[{"name":"Equipe de Chimie Th\u00e9orique, Electrochimie et Environnement CT2E, Facult\u00e9 des Sciences, Universit\u00e9 Ibn Zohr, Agadir, Maroc"}]},{"given":"Malika","family":"Bourjila","sequence":"additional","affiliation":[{"name":"Equipe de Chimie Th\u00e9orique, Electrochimie et Environnement CT2E, Facult\u00e9 des Sciences, Universit\u00e9 Ibn Zohr, Agadir, Maroc"}]},{"given":"Rachid Drissi","family":"El Bouzaidi","sequence":"additional","affiliation":[{"name":"Equipe de Chimie Th\u00e9orique, Electrochimie et Environnement CT2E, Facult\u00e9 des Sciences, Universit\u00e9 Ibn Zohr, Agadir, Maroc"},{"name":"Centre R\u00e9gional des M\u00e9tiers de L\u2019Education et de la Formation (CRMEF), Souss Massa Daraa, Inezgane, Maroc"}]},{"given":"Abderrahman","family":"El Gridani","sequence":"additional","affiliation":[{"name":"Equipe de Chimie Th\u00e9orique, Electrochimie et Environnement CT2E, Facult\u00e9 des Sciences, Universit\u00e9 Ibn Zohr, Agadir, Maroc"}]}],"member":"55691","reference":[{"key":"10.3233\/JCM-170735_ref1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/0002-9149(89)91193-4","article-title":"Ionic mechanisms of the depression of automaticity and conduction in the rabbit atrioventricular node caused by hypoxia or metabolic inhibition and protective action of glucose and valine","volume":"64","author":"Nishimura","year":"1989","journal-title":"American Journal of Cardiology"},{"key":"10.3233\/JCM-170735_ref2","doi-asserted-by":"crossref","first-page":"2488","DOI":"10.1093\/jn\/131.9.2488S","article-title":"Interaction between glutamine availability and metabolism of glycogen, tricarboxylic acid cycle intermediates and glutathione","volume":"131","author":"Rennie","year":"2001","journal-title":"Journal of Nutrition"},{"key":"10.3233\/JCM-170735_ref3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.amjcard.2008.02.064","article-title":"More than bricks and mortar: Comments on protein and amino acid metabolism in the heart","volume":"101","author":"Taegtmeyer","year":"2008","journal-title":"American Journal of Cardiology"},{"key":"10.3233\/JCM-170735_ref4","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1093\/ajcn\/78.2.250","article-title":"Essential amino acids are primarily responsible for the amino acid stimulation of muscle protein anabolism in healthy elderly adults","volume":"78","author":"Volpi","year":"2003","journal-title":"American Journal of Clinical Nutrition"},{"key":"10.3233\/JCM-170735_ref5","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1006\/jmbi.1993.1144","article-title":"Structure due to an aromatic-amide interaction observed by H-nuclear magnetic resonance spectroscopy: Peptides related to the N terminus of bovine pancreatic trypsin inhibitor","volume":"230","author":"kemmink","year":"1993","journal-title":"Journal of Molecular Biology"},{"key":"10.3233\/JCM-170735_ref6","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1006\/jmbi.1993.1631","article-title":"Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding","volume":"234","author":"Kemmink","year":"1993","journal-title":"Journal of Molecular Biology"},{"key":"10.3233\/JCM-170735_ref7","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1006\/jmbi.1994.0021","article-title":"The physical properties of local interactions of tyrosine residues in peptides and unfolded proteins","volume":"243","author":"Kemmink","year":"1995","journal-title":"Journal of Molecular Biology"},{"key":"10.3233\/JCM-170735_ref8","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/nature02261","article-title":"Protein folding and misfolding","volume":"426","author":"Dobson","year":"2003","journal-title":"Nature"},{"key":"10.3233\/JCM-170735_ref9","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1038\/nature02264","article-title":"Folding proteins in fatal ways","volume":"426","author":"Selkoe","year":"2003","journal-title":"Nature"},{"key":"10.3233\/JCM-170735_ref10","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1002\/qua.956","article-title":"Data mining, ab initio, and molecular mechanics study on conformation of phenylalanine and its interaction with neighboring backbone amide groups in proteins","volume":"90","author":"Duan","year":"2002","journal-title":"International Journal of Quantum Chemistry"},{"key":"10.3233\/JCM-170735_ref11","doi-asserted-by":"crossref","unstructured":"A. Abo-Riziq, L. Grace, B. Crews, M.P. Callahan, T. Van Mourik and M.S. De Vries, Conformational structure of tyrosine, tyrosyl-glycine, and tyrosyl-glycyl-glycine by double resonance spectroscopy, Journal of Physical Chemistry A115 (2011), 6077\u20136087.","DOI":"10.1021\/jp110601w"},{"key":"10.3233\/JCM-170735_ref12","doi-asserted-by":"crossref","unstructured":"IUPAC-IUB Commission on Biochemical Nomenclature, Abbreviations and symbols for the description of the conformation of polypeptide chains, Biochemistry 9 (1970), 3471\u20133479.","DOI":"10.1021\/bi00820a001"},{"key":"10.3233\/JCM-170735_ref13","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/S0166-1280(02)00497-9","article-title":"An assessment of the chiral environment created by adjacent D- and L-alanyl residues on a glycine unit within the tripeptide N-Ac-Ala-Gly-Ala-NHMe: An ab initio exploratory study","volume":"621","author":"Liao","year":"2003","journal-title":"Journal of Molecular Structure"},{"key":"10.3233\/JCM-170735_ref14","doi-asserted-by":"crossref","unstructured":"A. Mehdizadeh, G.A. Chass, \u00d6. Farkas, A. Perczel, L.L. Torday, A. Varro and J.G. Papp, Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMetripeptide motif: An ab initio exploratory study, Journal of Molecular Structure 588 (2002), 187\u2013200.","DOI":"10.1016\/S0166-1280(02)00172-0"},{"key":"10.3233\/JCM-170735_ref15","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1080\/00268970500465274","article-title":"The structure of the gas-phase tyrosine-glycine dipeptide","volume":"104","author":"Toroz","year":"2006","journal-title":"Molecular Physics"},{"key":"10.3233\/JCM-170735_ref16","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1080\/00268970601138762","article-title":"The structure of the gas-phase tyrosine-glycine-glycine tripeptide","volume":"105","author":"Toroz","year":"2007","journal-title":"Molecular Physics"},{"key":"10.3233\/JCM-170735_ref17","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/S0166-1280(00)00360-2","article-title":"Side-chain conformational analysis of N-formyl-l-asparaginamide and N-acetyl-l-asparagine N-methylamide in their \u03b3l backbone conformation","volume":"504","author":"Berg","year":"2000","journal-title":"Journal of Molecular Structure"},{"key":"10.3233\/JCM-170735_ref18","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1139\/v02-076","article-title":"Peptide model XXVIII: An exploratory ab initio and density functional study on the side-chain-backbone interaction in N-acetyl-L-cysteine-N-methylamide and N-formyl-L-cysteinamide in their \u03b3L-backbone conformations","volume":"80","author":"Zamora","year":"2002","journal-title":"Canadian Journal of Chemistry"},{"key":"10.3233\/JCM-170735_ref19","doi-asserted-by":"crossref","first-page":"5281","DOI":"10.1021\/jp048037j","article-title":"The gas-phase dipeptide analogue acetyl-phenylalanyl-amide: A model for the study of side chain\/backbone interactions in Proteins","volume":"A109","author":"Chin","year":"2005","journal-title":"Journal of Physical Chemistry"},{"key":"10.3233\/JCM-170735_ref20","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.theochem.2004.11.040","article-title":"Comprehensive conformational analysis of N-acetyl-l-tryptophane-N-methylamide, an ab initio and DFT study","volume":"724","author":"Bombasaro","year":"2005","journal-title":"Journal of Molecular Structure"},{"key":"10.3233\/JCM-170735_ref21","doi-asserted-by":"crossref","first-page":"6256","DOI":"10.1021\/ja00016a049","article-title":"Peptide models 1, topology of selected peptide conformational potential energy surfaces (glycine and alanine derivatives)","volume":"113","author":"Perczel","year":"1991","journal-title":"Journal of the American Chemical Society"},{"key":"10.3233\/JCM-170735_ref22","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/0166-1280(94)03929-F","article-title":"Peptide models XIII. Side-chain conformational energy surface E=E\u2062(\u03c71,\u03c72) of N-formyl-l-serinamide (For-l-Ser-NH2) in its \u03b3Lor Ceq7 backbone conformation","volume":"331","author":"Farkas","year":"1995","journal-title":"Journal of Molecular Structure"},{"key":"10.3233\/JCM-170735_ref23","doi-asserted-by":"crossref","unstructured":"B. El Merbouh, M. Bourjila, R. Tijar, R.D. El Bouzaidi, A. EL Gridani and M. El Mouhtadi, Conformational space analysis of neutral and protonated glycine using a genetic algorithm for multi-modal search, Journal of Theoretical and Computational Chemistry 13 (2014), 1450067\/1\u20131450067\/16.","DOI":"10.1142\/S0219633614500679"},{"key":"10.3233\/JCM-170735_ref24","unstructured":"A. El Guerdaoui, B. El Merbouh, R. Tijar, M. Bourjila, R.D. El Bouzaidi, A. EL Gridani and M. El Mouhtadi, An exhaustive conformational analysis of N-formyl-L-tyrosinamide using a genetic algorithm for multimodal search, Comptes Rendus Chimie (2016). doi: 101016\/j.crci.2016.11.008."},{"key":"10.3233\/JCM-170735_ref25","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1162\/evco.1994.2.4.321","article-title":"Multiniche crowding in genetic algorithms and its application to the assembly of DNA restriction-fragments","volume":"2","author":"Cedeno","year":"1995","journal-title":"Evolutionary Computation"},{"key":"10.3233\/JCM-170735_ref26","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/jcc.540100208","article-title":"Optimization of parameters for semiempirical methods I","volume":"10","author":"Stewart","year":"1988","journal-title":"Journal of Computational Chemistry"},{"key":"10.3233\/JCM-170735_ref27","unstructured":"K. Deb, Multi-objective optimization using evolutionary algorithms, in: Chicheter, J. Wiley & Sons, ed., 2001."},{"key":"10.3233\/JCM-170735_ref29","first-page":"3098","article-title":"Density-functional exchange-energy approximation with correct asymptotic behavior","volume":"A38","author":"Becke","year":"1998","journal-title":"Physical Review"},{"key":"10.3233\/JCM-170735_ref30","doi-asserted-by":"crossref","first-page":"5648","DOI":"10.1063\/1.464913","article-title":"Density-functional thermochemistry III, The role of exact exchange","volume":"98","author":"Becke","year":"1993","journal-title":"Journal of Chemical Physics"},{"key":"10.3233\/JCM-170735_ref31","first-page":"785","article-title":"Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density","volume":"B37","author":"Lee","year":"1998","journal-title":"Physical Review"},{"key":"10.3233\/JCM-170735_ref32","doi-asserted-by":"crossref","first-page":"2541","DOI":"10.1063\/1.1337861","article-title":"The conformational behavior of polyglycine as predicted by a density functional model with periodic boundary conditions","volume":"114","author":"Improta","year":"2001","journal-title":"Journal of Chemical Physics"},{"key":"10.3233\/JCM-170735_ref33","doi-asserted-by":"crossref","first-page":"7727","DOI":"10.1063\/1.480161","article-title":"Anisotropic intermolecular interactions in van der Waals and hydrogen-bonded complexes: What can we get from density functional calculations","volume":"111","author":"Millet","year":"1999","journal-title":"Journal of Chemical Physics"},{"key":"10.3233\/JCM-170735_ref34","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1007\/s002140000163","article-title":"Performance of recently developed kinetic energy density functionals for the calculation of hydrogen binding strengths and hydrogen-bonded structures","volume":"104","author":"Rabuck","year":"2000","journal-title":"Theoretical Chemistry Accounts"},{"key":"10.3233\/JCM-170735_ref36","doi-asserted-by":"crossref","unstructured":"I. Jakli, A. Perczel, \u00d6. Farkas, C.P. Sosa and I.G. Csizmadia, Peptide models XXIII, Conformational model for polar side-chain containing amino acid residues: A comprehensive analysis of RHF, DFT, and MP2 properties of HCO-L-SER-NH2, Journal of Computational Chemistry 21 (2000), 626\u2013655.","DOI":"10.1002\/(SICI)1096-987X(200006)21:8<626::AID-JCC4>3.0.CO;2-P"},{"key":"10.3233\/JCM-170735_ref37","first-page":"666","article-title":"An ab initio exploratory study of the full conformational space of MeCO-L-threonine-NH-Me","volume":"252","author":"Sahai","year":"2003","journal-title":"Journal of Molecular Structure"},{"key":"10.3233\/JCM-170735_ref38","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1093\/nar\/gks1200","article-title":"The RCSB protein data bank: New resources for research and education","volume":"41","author":"Rose","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"10.3233\/JCM-170735_ref39","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/S0166-1280(98)00222-X","article-title":"Peptide models XXII, A conformational model for aromatic amino acid residues in proteins, A comprehensive analysis of all the RHF\/6-31+G* conformers of For-L-Phe-NH2","volume":"455","author":"Jakli","year":"1998","journal-title":"Journal of Molecular Structure"},{"key":"10.3233\/JCM-170735_ref40","doi-asserted-by":"crossref","first-page":"5079","DOI":"10.1021\/jp030111v","article-title":"Exploration of the conformational space of N-Acetyl-L-glutamine-N-methylamide, An ab Initio and Density Functional Theory Study","volume":"A107","author":"Klipfel","year":"2003","journal-title":"Journal of Physical Chemistry"}],"container-title":["Journal of Computational Methods in Sciences and Engineering"],"original-title":[],"link":[{"URL":"https:\/\/content.iospress.com\/download?id=10.3233\/JCM-170735","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T22:07:13Z","timestamp":1776809233000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/full\/10.3233\/JCM-170735"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,8]]},"references-count":38,"journal-issue":{"issue":"3"},"URL":"https:\/\/doi.org\/10.3233\/jcm-170735","relation":{},"ISSN":["1472-7978","1875-8983"],"issn-type":[{"value":"1472-7978","type":"print"},{"value":"1875-8983","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,8]]}}}