Literature DB >> 24315087

Foundations of biomolecular modeling.

William L Jorgensen1.   

Abstract

The 2013 Nobel Prize in Chemistry has been awarded to Martin Karplus, Michael Levitt, and Arieh Warshel for "development of multiscale models for complex chemical systems." The honored work from the 1970s has provided a foundation for the widespread activities today in modeling organic and biomolecular systems.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID： 24315087      PMCID： PMC3892588          DOI： 10.1016/j.cell.2013.11.023

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  11 in total

1.  Computer simulation of protein folding.

Authors:  M Levitt; A Warshel
Journal:  Nature       Date:  1975-02-27       Impact factor: 49.962

Review 2.  Perspective on the Martini model.

Authors:  Siewert J Marrink; D Peter Tieleman
Journal:  Chem Soc Rev       Date:  2013-08-21       Impact factor: 54.564

3.  Accurate statistical associating fluid theory for chain molecules formed from Mie segments.

Authors:  Thomas Lafitte; Anastasia Apostolakou; Carlos Avendaño; Amparo Galindo; Claire S Adjiman; Erich A Müller; George Jackson
Journal:  J Chem Phys       Date:  2013-10-21       Impact factor: 3.488

4.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

Authors:  A Warshel; M Levitt
Journal:  J Mol Biol       Date:  1976-05-15       Impact factor: 5.469

5.  Understanding molecular structure from molecular mechanics.

Authors:  Norman L Allinger
Journal:  J Comput Aided Mol Des       Date:  2011-04-10       Impact factor: 3.686

6.  A simplified representation of protein conformations for rapid simulation of protein folding.

Authors:  M Levitt
Journal:  J Mol Biol       Date:  1976-06-14       Impact factor: 5.469

Review 7.  Protein folding.

Authors:  G Némethy; H A Scheraga
Journal:  Q Rev Biophys       Date:  1977-08       Impact factor: 5.318

8.  Implications of torsional potential of retinal isomers for visual excitation.

Authors:  B Honig; M Karplus
Journal:  Nature       Date:  1971-02-19       Impact factor: 49.962

9.  Refinement of protein conformations using a macromolecular energy minimization procedure.

Authors:  M Levitt; S Lifson
Journal:  J Mol Biol       Date:  1969-12-14       Impact factor: 5.469

10.  On the formation of protein tertiary structure on a computer.

Authors:  A T Hagler; B Honig
Journal:  Proc Natl Acad Sci U S A       Date:  1978-02       Impact factor: 11.205
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  10 in total

1.  Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Authors:  Jonah Z Vilseck; Jakub Kostal; Julian Tirado-Rives; William L Jorgensen
Journal:  J Comput Chem       Date:  2015-08-27       Impact factor: 3.376

2.  SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

Authors:  Lane W Votapka; Benjamin R Jagger; Alexandra L Heyneman; Rommie E Amaro
Journal:  J Phys Chem B       Date:  2017-03-03       Impact factor: 2.991

3.  Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule.

Authors:  Pedro A Sánchez-Murcia; Alberto Mills; Álvaro Cortés-Cabrera; Federico Gago
Journal:  J Comput Aided Mol Des       Date:  2019-05-31       Impact factor: 3.686

4.  Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17).

Authors:  Subrata Pramanik; Arne Kutzner; Klaus Heese
Journal:  Tumour Biol       Date:  2014-09-20

5.  Interactions of cantharidin-like inhibitors with human protein phosphatase-5 in a Mg2+ system: molecular dynamics and quantum calculations.

Authors:  Letícia C Assis; Alexandre A de Castro; Ingrid G Prandi; Daiana T Mancini; Juliana O S de Giacoppo; Ranylson M L Savedra; Tamiris M de Assis; Juliano B Carregal; Elaine F F da Cunha; Teodorico Castro Ramalho
Journal:  J Mol Model       Date:  2018-10-02       Impact factor: 1.810

6.  General van der Waals potential for common organic molecules.

Authors:  Rui Qi; Qiantao Wang; Pengyu Ren
Journal:  Bioorg Med Chem       Date:  2016-08-02       Impact factor: 3.641

Review 7.  Design and application of implicit solvent models in biomolecular simulations.

Authors:  Jens Kleinjung; Franca Fraternali
Journal:  Curr Opin Struct Biol       Date:  2014-05-20       Impact factor: 6.809

8.  Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.

Authors:  M Olivia Kim; Patrick G Blachly; Joseph W Kaus; J Andrew McCammon
Journal:  J Phys Chem B       Date:  2014-08-25       Impact factor: 2.991

9.  The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

Authors:  Sergio Decherchi; Anna Berteotti; Giovanni Bottegoni; Walter Rocchia; Andrea Cavalli
Journal:  Nat Commun       Date:  2015-01-27       Impact factor: 14.919

10.  Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

Authors:  Lane W Votapka; Rommie E Amaro
Journal:  PLoS Comput Biol       Date:  2015-10-27       Impact factor: 4.475
  10 in total

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