Proceedings of the Genetic and Evolutionary Computation Conference 2019
DOI: 10.1145/3321707.3321777
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Using subpopulation EAs to map molecular structure landscapes

Abstract: The emerging view in molecular biology is that molecules are intrinsically dynamic systems rearranging themselves into different structures to interact with molecules in the cell. Such rearrangements take place on energy landscapes that are vast and multimodal, with minima housing alternative structures. The multiplicity of biologically-active structures is prompting researchers to expand their treatment of classic computational biology problems, such as the template-free protein structure prediction problem (… Show more

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Cited by 6 publications
(5 citation statements)
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References 31 publications
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“…Great algorithmic advances have been made in structure generation, most remarkably by Rosetta [10], Quark [11], and others [12][13][14][15][16]. Recent works have investigated incorporating complementary information like sequence-predicted contacts and constructing new energy functions based on predicted contacts or distances of pairs of amino acids for structure generation [17][18][19].…”
Section: Introductionmentioning
confidence: 99%
See 1 more Smart Citation
“…Great algorithmic advances have been made in structure generation, most remarkably by Rosetta [10], Quark [11], and others [12][13][14][15][16]. Recent works have investigated incorporating complementary information like sequence-predicted contacts and constructing new energy functions based on predicted contacts or distances of pairs of amino acids for structure generation [17][18][19].…”
Section: Introductionmentioning
confidence: 99%
“…Great progress in software and hardware have made it less costly to generate structures. For instance, algorithms operating under the umbrella of evolutionary computation can generate hundreds of thousands of structures [12,13,16,17]. Algorithms tasked with analyzing these structures now may have to additionally deal with a data size issue.…”
Section: Introductionmentioning
confidence: 99%
“…Good advances have been made in decoy generation [10,[16][17][18][23][24][25][26]. These advances are documented in the Critical Assessment of protein Structure Prediction (CASP), which is a biennial community experiment/competition that assesses progress in PSP in several categories, including the template-free/free modeling category [9].…”
Section: Introductionmentioning
confidence: 99%
“…Great progress in software and hardware has made it less costly to generate decoys. Algorithms operating under the umbrella of evolutionary computation can generate hundreds of thousands of decoys [17,[24][25][26]. Decoy selection algorithms tasked with analyzing decoys now may have to additionally deal with a data size issue.…”
Section: Introductionmentioning
confidence: 99%
“…One is Rosetta's Simulated Annealing Metropolis Monte Carlo (SA-MMC) based decoy sampling algorithm. The other is a recent subpopulation EA, SP-EA + [20], that aims to prevent premature convergence and retain diversity during optimization by evolving and maintaining multiple subpopulations.…”
Section: Methodsmentioning
confidence: 99%