Research Topics
| Marcos R BetancourtSummaryAffiliation: Indiana University Purdue University Indianapolis Country: USA Publications
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Detail Information
Publications
Optimization of Monte Carlo trial moves for protein simulationsMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, 402 N Blackford St, LD156 J Indianapolis, Indiana 46202, USA
J Chem Phys 134:014104. 2011..By assigning distributions that generate a smaller number of moving residues to lower temperature replicas, the simulation times are decreased as long as the higher temperature replicas are effective...- Comparison between molecular dynamic based and knowledge based potentials for protein side chainsMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
J Comput Biol 17:943-52. 2010..Among the molecular dynamic-based potentials, the one derived using the G43A2 force field resulted in the highest prediction accuracy... - Empirical model of residue contact probabilities for polypeptidesMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, 402 N Blackford St, LD156 J, Indianapolis, Indiana 46202, USA
J Chem Phys 132:085101. 2010..Overall, contacts with loop lengths above 33 residues behave as those from random flight chains. One exception are polyproline chains for which this length seems to be much higher... - Pairwise energies for polypeptide coarse-grained models derived from atomic force fieldsMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, 402 N Blackford St, LD156 J Indianapolis, Indiana 46202, USA
J Chem Phys 130:195103. 2009..In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field... - Another look at the conditions for the extraction of protein knowledge-based potentialsMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
Proteins 76:72-85. 2009.... - Knowledge-based potential for the polypeptide backboneMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, 402 N Blackford Street, LD156 J, Indianapolis, Indiana 46202, USA
J Phys Chem B 112:5058-69. 2008..In particular, the entropy difference between alanine and glycine agrees with the ones computed from molecular dynamics simulations ( approximately 0.4 kcal/mol)... - Efficient Monte Carlo trial moves for polypeptide simulationsMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
J Chem Phys 123:174905. 2005..The FEMs, combined with pivot moves, are used in a test to fold a group of coarse-grained proteins with lengths of up to 200 residues... - Local propensities and statistical potentials of backbone dihedral angles in proteinsMarcos R Betancourt
University at Buffalo Center of Excellence in Bioinformatics, 901 Washington St, Suite 300, Buffalo, NY 14203, USA
J Mol Biol 342:635-49. 2004..In general, most alpha-helices and many beta-sheets are strongly determined by the local potential, while the conformations in loops and near the end of beta-sheets are more influenced by non-local interactions... - A reduced protein model with accurate native-structure identification abilityMarcos R Betancourt
University at Buffalo Center of Excellence in Bioinformatics, Buffalo, New York 14203, USA
Proteins 53:889-907. 2003..The results indicate that the pseudoatomic model has native recognition ability similar to comparable atomic-based models but much better than equivalent residue-based models... - Coarse-grained protein model with residue orientation energies derived from atomic force fieldsMarcos R Betancourt
Department of Physics, Indiana University Purdue University Indianapolis, 402 North Blackford Street LD156 J, Indianapolis, Indiana 46202, USA
J Phys Chem B 113:14824-30. 2009..It is also found that a careful balance between local and nonlocal interactions is essential. Possibilities for improving coarse-grained models derived from atomic force fields are discussed...