1997
DOI: 10.1021/ma970662h
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Efficient Method To Count and Generate Compact Protein Lattice Conformations

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Cited by 19 publications
(10 citation statements)
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“…14 Network representations of protein structures have been employed in the past. [15][16][17][18][19] Brinda et al represented each amino acid in a protein structure by a node and the noncovalent interaction strength between two amino acids was considered in the determination of edges. 20 The constructed representations were called protein structure graphs (PSGs).…”
Section: Introductionmentioning
confidence: 99%
“…14 Network representations of protein structures have been employed in the past. [15][16][17][18][19] Brinda et al represented each amino acid in a protein structure by a node and the noncovalent interaction strength between two amino acids was considered in the determination of edges. 20 The constructed representations were called protein structure graphs (PSGs).…”
Section: Introductionmentioning
confidence: 99%
“…Additionally, amino acids in proteins are covalently linked, forming sequences usually containing between tens to hundreds of residues. The simplest mathematical models that mimic the linear nature of the protein sequence, its tight packing in the native state and the exclusion volume effect are compact self-avoiding walks on lattices (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). The compact self-avoiding walk requires that each of the lattice points must be visited once and only once.…”
Section: Introductionmentioning
confidence: 99%
“…For very simple discrete models, all conformations could be enumerated [20,76,96,141,[255][256][257][258][259][260] and an exact analysis of the model thermodynamics performed [20,261]. Structure and thermodynamics of more complex models are studied via classical molecular dynamics [262 -267] (MD), Monte Carlo (MC) methods [26,109,129,158 -160,167,168, 237,239,268-274], genetic algorithms and hybrid combinations of these methods [275].…”
Section: Sampling Conformational Space Of Reduced Modelsmentioning
confidence: 99%