Literature DB >> 30176213

Tinker 8: Software Tools for Molecular Design.

Joshua A Rackers1, Zhi Wang2, Chao Lu2, Marie L Laury2, Louis Lagardère3, Michael J Schnieders4, Jean-Philip Piquemal3, Pengyu Ren5, Jay W Ponder1,2.   

Abstract

The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.

Entities:  

Year:  2018        PMID: 30176213      PMCID: PMC6335969          DOI: 10.1021/acs.jctc.8b00529

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  84 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Electrostatics of nanosystems: application to microtubules and the ribosome.

Authors:  N A Baker; D Sept; S Joseph; M J Holst; J A McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

Review 3.  Potential energy functions: from consistent force fields to spectroscopically determined polarizable force fields.

Authors:  Kim Palmo; Berit Mannfors; Noemi G Mirkin; Samuel Krimm
Journal:  Biopolymers       Date:  2003-03       Impact factor: 2.505

4.  Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes.

Authors:  Michael Schaefer; Christian Bartels; Fabrice Leclerc; Martin Karplus
Journal:  J Comput Chem       Date:  2001-11-30       Impact factor: 3.376

5.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Authors:  Vijay S Pande; Ian Baker; Jarrod Chapman; Sidney P Elmer; Siraj Khaliq; Stefan M Larson; Young Min Rhee; Michael R Shirts; Christopher D Snow; Eric J Sorin; Bojan Zagrovic
Journal:  Biopolymers       Date:  2003-01       Impact factor: 2.505

6.  Effective Born radii in the generalized Born approximation: the importance of being perfect.

Authors:  Alexey Onufriev; David A Case; Donald Bashford
Journal:  J Comput Chem       Date:  2002-11-15       Impact factor: 3.376

7.  Atomic solvation parameters applied to molecular dynamics of proteins in solution.

Authors:  L Wesson; D Eisenberg
Journal:  Protein Sci       Date:  1992-02       Impact factor: 6.725

8.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

Authors:  T E Cheatham; P Cieplak; P A Kollman
Journal:  J Biomol Struct Dyn       Date:  1999-02

9.  The functional form of angular forces around transition metal ions in biomolecules.

Authors:  A E Carlsson; S Zapata
Journal:  Biophys J       Date:  2001-07       Impact factor: 4.033

10.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

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  68 in total

1.  AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2019-06-11       Impact factor: 6.006

2.  Computational and Experimental Studies of Inhibitor Design for Aldolase A.

Authors:  Rui Qi; Brandon Walker; Zhifeng Jing; Maiya Yu; Gabriel Stancu; Ramakrishna Edupuganti; Kevin N Dalby; Pengyu Ren
Journal:  J Phys Chem B       Date:  2019-07-03       Impact factor: 2.991

3.  Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.

Authors:  Zhifeng Jing; Rui Qi; Marc Thibonnier; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2019-10-09       Impact factor: 6.006

4.  Classical Pauli repulsion: An anisotropic, atomic multipole model.

Authors:  Joshua A Rackers; Jay W Ponder
Journal:  J Chem Phys       Date:  2019-02-28       Impact factor: 3.488

5.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

6.  Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field.

Authors:  Marie L Laury; Zhi Wang; Aaron S Gordon; Jay W Ponder
Journal:  J Comput Aided Mol Des       Date:  2018-10-15       Impact factor: 3.686

7.  LICHEM 1.1: Recent Improvements and New Capabilities.

Authors:  Hatice Gökcan; Erik Antonio Vázquez-Montelongo; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2019-04-02       Impact factor: 6.006

8.  Virial Based Berendsen Barostat on GPUs using AMOEBA in Tinker-OpenMM.

Authors:  Matthew Harger; Pengyu Ren
Journal:  Results Chem       Date:  2019-06-20

9.  Experimental and theoretical characterization of the strong effects on DNA stability caused by half-sandwich Ru(II) and Ir(III) bearing thiabendazole complexes.

Authors:  Javier Santolaya; Natalia Busto; Marta Martínez-Alonso; Gustavo Espino; Jörg Grunenberg; Giampaolo Barone; Begoña García
Journal:  J Biol Inorg Chem       Date:  2020-09-20       Impact factor: 3.358

10.  Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations.

Authors:  Léa El Khoury; Frédéric Célerse; Louis Lagardère; Luc-Henri Jolly; Etienne Derat; Zeina Hobaika; Richard G Maroun; Pengyu Ren; Serge Bouaziz; Nohad Gresh; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2020-03-30       Impact factor: 6.006

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