Computational Approaches to Biochemical Reactivity

Náray‐Szabó, Gábor; Warshel, Arieh

doi:10.1007/0-306-46934-0

Cited by 18 publications

References 476 publications

(688 reference statements)

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Efficiency of tabu‐search‐based conformational search algorithms

et al. 2011

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Efficient conformational search or sampling approaches play an integral role in molecular modeling, leading to a strong demand for even faster and more reliable conformer search algorithms. This article compares the efficiency of a molecular dynamics method, a simulated annealing method, and the basin hopping (BH) approach (which are widely used in this field) with a previously suggested tabu-search-based approach called gradient only tabu search (GOTS). The study emphasizes the success of the GOTS procedure and, more importantly, shows that an approach which combines BH and GOTS outperforms the single methods in efficiency and speed. We also show that ring structures built by a hydrogen bond are useful as starting points for conformational search investigations of peptides and organic ligands with biological activities, especially in structures that contain multiple rings.

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Efficiency of tabu‐search‐based conformational search algorithms

et al. 2011

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Monte Carlo Method for Calculating the Electrostatic Energy of a Molecule

Mascagni

Simonov

2003

Lecture Notes in Computer Science

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Abstract. The problem of computing the electrostatic energy of a large molecule is considered. It is reduced to solving the Poisson equation inside and the linear Poisson-Boltzmann equation in the exterior, coupled by boundary conditions. A Monte Carlo estimate for the potential point values, their derivatives, and the energy is constructed. The estimate is based on the walk on spheres and Green's function first passage algorithms; the walk in subdomains technique; and finite-difference approximations of the boundary condition. Results of some illustrative calculations are presented.

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