Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology 2003
DOI: 10.1145/640075.640099
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Cited by 135 publications
(154 citation statements)
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“…The Markov chain can then be started at this conformation, and all states sampled will have the same knot. The set of pull moves [36], extended to ring polymers, is such a move set. In pull moves, a bead is moved to a site adjacent to one of its two neighbours: we refer to the direction of the chosen neighbour as 'up' the chain.…”
Section: B Pull Movesmentioning
confidence: 99%
See 1 more Smart Citation
“…The Markov chain can then be started at this conformation, and all states sampled will have the same knot. The set of pull moves [36], extended to ring polymers, is such a move set. In pull moves, a bead is moved to a site adjacent to one of its two neighbours: we refer to the direction of the chosen neighbour as 'up' the chain.…”
Section: B Pull Movesmentioning
confidence: 99%
“…2. More details, and applications to the simulation of lattice polymers and peptides, may be found elsewhere [28,36]; we have recently improved some aspects of the algorithm [29] and here we use the "unbiased pull moves" of that paper.…”
Section: B Pull Movesmentioning
confidence: 99%
“…Therefore, sophisticated algorithms were developed to find lowest-energy states for chains of up to 136 monomers. The methods applied are based on very different algorithms, ranging from exact enumeration in two dimensions [11,12] and three dimensions on cuboid (compact) lattices [4,[13][14][15], and hydrophobic-core construction methods [16,17] over genetic algorithms [18][19][20][21][22], Monte Carlo simulations with different types of move sets [23][24][25][26], and generalized ensemble approaches [27] to Rosenbluth chaingrowth methods [28] of the 'Go with the Winners' type [29][30][31][32][33][34][35]. With some of these algorithms, thermodynamic quantities of lattice heteropolymers were studied as well [14,27,31,[34][35][36].…”
Section: The Hydrophobic-polar (Hp) Lattice Protein Modelmentioning
confidence: 99%
“…This way the replicas change temperature based on their energy level. The set of moves used by REMC-HPPFP to perturbate the candidate configurations comprises a set of standard residue by residue moves, termed VHSD moves, and the non-standard pull move [9]. This set of moves is the most complete and efficient set of moves available to date for the HP model on the square and cubic lattices.…”
Section: Remc-hppfpmentioning
confidence: 99%