Literature DB >> 20387919

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

Satoru G Itoh1, Hisashi Okumura, Yuko Okamoto.   

Abstract

We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical and replica-exchange methods.

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Year:  2010        PMID： 20387919     DOI： 10.1063/1.3372767

Source DB:  PubMed          Journal:  J Chem Phys        ISSN： 0021-9606            Impact factor:   3.488


  15 in total

1.  pH replica-exchange method based on discrete protonation states.

Authors:  Satoru G Itoh; Ana Damjanović; Bernard R Brooks
Journal:  Proteins       Date:  2011-10-15

Review 2.  Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

Authors:  Jinzen Ikebe; Koji Umezawa; Junichi Higo
Journal:  Biophys Rev       Date:  2016-01-11

3.  Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

Authors:  Xiongwu Wu; Milan Hodoscek; Bernard R Brooks
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

4.  Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.

Authors:  Naohiro Nishikawa; Kyungreem Han; Xiongwu Wu; Florentina Tofoleanu; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-15       Impact factor: 3.686

5.  Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

Authors:  Ilja V Khavrutskii; Anders Wallqvist
Journal:  J Chem Theory Comput       Date:  2010-11-09       Impact factor: 6.006

Review 6.  All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations.

Authors:  Satoru G Itoh; Hisashi Okumura
Journal:  Methods Mol Biol       Date:  2022

7.  Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Authors:  Florentina Tofoleanu; Juyong Lee; Frank C Pickard Iv; Gerhard König; Jing Huang; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-30       Impact factor: 3.686

8.  Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Authors:  Juyong Lee; Florentina Tofoleanu; Frank C Pickard; Gerhard König; Jing Huang; Ana Damjanović; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

9.  GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

Authors:  Jaewoon Jung; Takaharu Mori; Chigusa Kobayashi; Yasuhiro Matsunaga; Takao Yoda; Michael Feig; Yuji Sugita
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2015-05-07

10.  Dynamic properties of SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases studied by molecular dynamics simulations.

Authors:  Satoru G Itoh; Shoichi Tanimoto; Hisashi Okumura
Journal:  Chem Phys Lett       Date:  2021-06-10       Impact factor: 2.328
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