Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

2017-amber15fb

Lee-Ping Wang; Keri A. McKiernan; Joseph Gomes; Kyle A. Beauchamp; Teresa Head-Gordon; Julia E. Rice; William C. Swope; Todd J. Martínez; Vijay S. Pande

2017-04-06 (online) – 2017-04-27 (print)

The Journal of Physical Chemistry B (J. Phys. Chem. B). 121, 16, 4023-4039. doi:10.1021/acs.jpcb.7b02320

forcefield

MSMBuilder: Statistical Models for Biomolecular Dynamics

2016-msmbuilder3

Matthew P. Harrigan; Mohammad M. Sultan; Carlos X. Hernández; Brooke E. Husic; Peter Eastman; Christian R. Schwantes; Kyle A. Beauchamp; Robert T. McGibbon; Vijay S. Pande

2017-01-01 (print)

Biophysical Journal (Biophys. J.). 112, 1, 10-15. doi:10.1016/j.bpj.2016.10.042

software

Osprey: Hyperparameter Optimization for Machine Learning

2016-osprey

Robert T. McGibbon; Carlos X. Hernández; Matthew P. Harrigan; Steven Kearnes; Mohammad M. Sultan; Stanislaw Jastrzebski; Brooke E. Husic; Vijay S. Pande

2016-09-07 (print)

The Journal of Open Source Software (The Journal of Open Source Software). 1, 5, doi:10.21105/joss.00034

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

2015-ensembler

Daniel L. Parton; Patrick B. Grinaway; Sonya M. Hanson; Kyle A. Beauchamp; John D. Chodera

2016-06-23 (online)

PLOS Computational Biology (PLoS Comput. Biol.). 12, 6, e1004728. doi:10.1371/journal.pcbi.1004728

Description

Automatic generation of homology models of protein families

TensorFlow: A system for large-scale machine learning

2016-tensorflow

Martín Abadi; Paul Barham; Jianmin Chen; Zhifeng Chen; Andy Davis; Jeffrey Dean; Matthieu Devin; Sanjay Ghemawat; Geoffrey Irving; Michael Isard; Manjunath Kudlur; Josh Levenberg; Rajat Monga; Sherry Moore; Derek G. Murray; Benoit Steiner; Paul Tucker; Vijay Vasudevan; Pete Warden; Martin Wicke; Yuan Yu; Xiaoqiang Zheng

2016-05-27 (online)

arxiv:1605.08695

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

2016-htmd

S. Doerr; M. J. Harvey; Frank Noé; G. De Fabritiis

2016-04-12 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 12, 4, 1845-1852. doi:10.1021/acs.jctc.6b00049

Description

This can make MSMs in addition to being a one-stop shop for running MD.

It's available under an academic license.

software python

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

2016-charmm-gui

Jumin Lee; Xi Cheng; Jason M. Swails; Min Sun Yeom; Peter K. Eastman; Justin A. Lemkul; Shuai Wei; Joshua Buckner; Jong Cheol Jeong; Yifei Qi; Sunhwan Jo; Vijay S. Pande; David A. Case; Charles L. Brooks; Alexander D. MacKerell; Jeffery B. Klauda; Wonpil Im

2016-01-12 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 12, 1, 405-413. doi:10.1021/acs.jctc.5b00935

software

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

2015-pyemma

Martin K. Scherer; Benjamin Trendelkamp-Schroer; Fabian Paul; Guillermo Pérez-Hernández; Moritz Hoffmann; Nuria Plattner; Christoph Wehmeyer; Jan-Hendrik Prinz; Frank Noé

2015-11-10 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 11, 11, 5525-5542. doi:10.1021/acs.jctc.5b00743

software python

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

2015-mdtraj

Robert T. McGibbon; Kyle A. Beauchamp; Matthew P. Harrigan; Christoph Klein; Jason M. Swails; Carlos X. Hernández; Christian R. Schwantes; Lee-Ping Wang; Thomas J. Lane; Vijay S. Pande

2015-10-01 (print)

Biophysical Journal (Biophys. J.). 109, 8, 1528-1532. doi:10.1016/j.bpj.2015.08.015

software python

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

2015-gromacs

Mark James Abraham; Teemu Murtola; Roland Schulz; Szilárd Páll; Jeremy C. Smith; Berk Hess; Erik Lindahl

2015-09-01 (print)

SoftwareX (SoftwareX). 1-2, 19-25. doi:10.1016/j.softx.2015.06.001

software

Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion

2014-moore-coarsegrain

Timothy C. Moore; Christopher R. Iacovella; Clare McCabe

2014-06-14 (print)

The Journal of Chemical Physics (J. Chem. Phys.). 140, 22, 224104. doi:10.1063/1.4880555

Description

Coarse-graining?

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

2014-forcebalance

Lee-Ping Wang; Todd J. Martinez; Vijay S. Pande

2014-06-05 (print)

The Journal of Physical Chemistry Letters (J. Phys. Chem. Lett.). 5, 11, 1885-1891. doi:10.1021/jz500737m

forcefield

Lipid14: The Amber Lipid Force Field

2014-lipid14

Callum J. Dickson; Benjamin D. Madej; Åge A. Skjevik; Robin M. Betz; Knut Teigen; Ian R. Gould; Ross C. Walker

2014-02-11 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 10, 2, 865-879. doi:10.1021/ct4010307

forcefield

Best Practices for Scientific Computing

2014-scicomp-best-practices

Greg Wilson; D. A. Aruliah; C. Titus Brown; Neil P. Chue Hong; Matt Davis; Richard T. Guy; Steven H. D. Haddock; Kathryn D. Huff; Ian M. Mitchell; Mark D. Plumbley; Ben Waugh; Ethan P. White; Paul Wilson

2014-01-07 (online)

PLoS Biology (PLoS Biol.). 12, 1, e1001745. doi:10.1371/journal.pbio.1001745

An exploratory study of the pull-based software development model

2014-pull-requests

Georgios Gousios; Martin Pinzger; Arie van Deursen

2014-01-01 (print)

Proceedings of the 36th International Conference on Software Engineering - ICSE 2014 (Proceedings of the 36th International Conference on Software Engineering - ICSE 2014). doi:10.1145/2568225.2568260

Description

Pull-request based development model

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

2013-openmm

Peter Eastman; Mark S. Friedrichs; John D. Chodera; Randall J. Radmer; Christopher M. Bruns; Joy P. Ku; Kyle A. Beauchamp; Thomas J. Lane; Lee-Ping Wang; Diwakar Shukla; Tony Tye; Mike Houston; Timo Stich; Christoph Klein; Michael R. Shirts; Vijay S. Pande

2013-01-08 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 9, 1, 461-469. doi:10.1021/ct300857j

software

EMMA: A Software Package for Markov Model Building and Analysis

2012-jemma

Martin Senne; Benjamin Trendelkamp-Schroer; Antonia S.J.S. Mey; Christof Schütte; Frank Noé

2012-07-10 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 8, 7, 2223-2238. doi:10.1021/ct300274u

Description

The previous, java version of EMMA. Look at 2015-pyemma instead.

software

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

2012-amber

Andreas W. Götz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le Grand; Ross C. Walker

2012-05-08 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 8, 5, 1542-1555. doi:10.1021/ct200909j

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

1999-ff99

Kyle A. Beauchamp; Yu-Shan Lin; Rhiju Das; Vijay S. Pande

2012-04-10 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 8, 4, 1409-1414. doi:10.1021/ct2007814

forcefield

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

2011-msmbuilder2

Kyle A. Beauchamp; Gregory R. Bowman; Thomas J. Lane; Lutz Maibaum; Imran S. Haque; Vijay S. Pande

2011-10-11 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 7, 10, 3412-3419. doi:10.1021/ct200463m

software

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

2011-mdanalysis

Naveen Michaud-Agrawal; Elizabeth J. Denning; Thomas B. Woolf; Oliver Beckstein

2011-04-15 (online) – 2011-07-30 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 32, 10, 2319-2327. doi:10.1002/jcc.21787

Scikit-learn: Machine Learning in Python

2011-sklearn

F. Pedregosa; G. Varoquaux; A. Gramfort; V. Michel; B. Thirion; O. Grisel; M. Blondel; P. Prettenhofer; R. Weiss; V. Dubourg; J. Vanderplas; A. Passos; D. Cournapeau; M. Brucher; M. Perrot; E. Duchesnay

2011-01-01 (print)

Journal of Machine Learning Research (J. Mach. Learn. Res.). 12, 2825-2830.

software python

Current Status of the AMOEBA Polarizable Force Field

2010-amoeba

Jay W. Ponder; Chuanjie Wu; Pengyu Ren; Vijay S. Pande; John D. Chodera; Michael J. Schnieders; Imran Haque; David L. Mobley; Daniel S. Lambrecht; Robert A. DiStasio; Martin Head-Gordon; Gary N. I. Clark; Margaret E. Johnson; Teresa Head-Gordon

2010-03-04 (print)

The Journal of Physical Chemistry B (J. Phys. Chem. B). 114, 8, 2549-2564. doi:10.1021/jp910674d

forcefield

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

2010-charmm27

Pär Bjelkmar; Per Larsson; Michel A. Cuendet; Berk Hess; Erik Lindahl

2010-02-09 (print)

Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 6, 2, 459-466. doi:10.1021/ct900549r

forcefield

Web-scale k-means clustering

2010-minibatch-kmeans

D. Sculley

2010-01-01 (print)

Proceedings of the 19th international conference on World wide web - WWW '10 (Proceedings of the 19th international conference on World wide web - WWW '10). doi:10.1145/1772690.1772862

Description

Clustering algorithm from sklearn admired for its speed.

algorithm

Using generalized ensemble simulations and Markov state models to identify conformational states

2009-msmbuilder1

Gregory R. Bowman; Xuhui Huang; Vijay S. Pande

2009-10-01 (print)

Methods (Methods). 49, 2, 197-201. doi:10.1016/j.ymeth.2009.04.013

Description

This introduced the first release of MSMBuilder. You probably shouldn't cite this unless you have a good reason to.

software python

Millisecond-scale molecular dynamics simulations on Anton

2009-anton

David E. Shaw; Kevin J. Bowers; Edmond Chow; Michael P. Eastwood; Douglas J. Ierardi; John L. Klepeis; Jeffrey S. Kuskin; Richard H. Larson; Kresten Lindorff-Larsen; Paul Maragakis; Mark A. Moraes; Ron O. Dror; Stefano Piana; Yibing Shan; Brian Towles; John K. Salmon; J. P. Grossman; Kenneth M. Mackenzie; Joseph A. Bank; Cliff Young; Martin M. Deneroff; Brannon Batson

2009-01-01 (print)

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis - SC '09 (Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis - SC '09). doi:10.1145/1654059.1654126

Limits on Variations in Protein Backbone Dynamics from Precise Measurements of Scalar Couplings

2007-scalar-coupling

Beat Vögeli; Jinfa Ying; Alexander Grishaev; Ad Bax

2007-08-01 (print)

Journal of the American Chemical Society (JACS). 129, 30, 9377-9385. doi:10.1021/ja070324o

IPython: A System for Interactive Scientific Computing

2007-ipython

Fernando Perez; Brian E. Granger

2007-01-01 (print)

Computing in Science & Engineering (Comput. Sci. Eng.). 9, 3, 21-29. doi:10.1109/MCSE.2007.53

software python

Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

2006-bowers-cluster

Kevin Bowers; Edmond Chow; Huafeng Xu; Ron Dror; Michael Eastwood; Brent Gregersen; John Klepeis; Istvan Kolossvary; Mark Moraes; Federico Sacerdoti; John Salmon; Yibing Shan; David Shaw

2006-11-01 (print)

ACM/IEEE SC 2006 Conference (SC'06) (ACM/IEEE SC 2006 Conference (SC'06)). doi:10.1109/SC.2006.54

A general purpose model for the condensed phases of water: TIP4P/2005

2005-tip4p

J. L. F. Abascal; C. Vega

2005-12-15 (print)

The Journal of Chemical Physics (J. Chem. Phys.). 123, 23, 234505. doi:10.1063/1.2121687

forcefield

Scalable molecular dynamics with NAMD

2005-namd

James C. Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant Kalé; Klaus Schulten

2005-01-01 (online) – 2005-12-01 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 26, 16, 1781-1802. doi:10.1002/jcc.20289

Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

2004-charmm27

Alexander D. Mackerell; Michael Feig; Charles L. Brooks

2004-08-01 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 25, 11, 1400-1415. doi:10.1002/jcc.20065

forcefield

Development and testing of a general amber force field

2004-gaff

Junmei Wang; Romain M. Wolf; James W. Caldwell; Peter A. Kollman; David A. Case

2004-01-01 (online) – 2004-07-15 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 25, 9, 1157-1174. doi:10.1002/jcc.20035

forcefield

Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm

2003-drude-particles

Guillaume Lamoureux; Benoı̂t Roux

2003-08-08 (print)

The Journal of Chemical Physics (J. Chem. Phys.). 119, 6, 3025-3039. doi:10.1063/1.1589749

forcefield

VMD: Visual molecular dynamics

1996-vmd

William Humphrey; Andrew Dalke; Klaus Schulten

1996-02-01 (print)

Journal of Molecular Graphics (J. Mol. Graph.). 14, 1, 33-38. doi:10.1016/0263-7855(96)00018-5

Description

The only game in town for making movies.

software

Knowledge-based protein secondary structure assignment

1995-stride

Dmitrij Frishman; Patrick Argos

1995-12-01 (print)

Proteins: Structure, Function, and Genetics (Proteins: Structure, Function, and Genetics). 23, 4, 566-579. doi:10.1002/prot.340230412

Description

VMD wants you to cite this for secondary structure prediction

software

Fast Parallel Algorithms for Short-Range Molecular Dynamics

1995-plimpton

Steve Plimpton

1995-03-01 (print)

Journal of Computational Physics (J. Comput. Phys.). 117, 1, 1-19. doi:10.1006/jcph.1995.1039

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

1992-wham

Shankar Kumar; John M. Rosenberg; Djamal Bouzida; Robert H. Swendsen; Peter A. Kollman

1992-10-01 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 13, 8, 1011-1021. doi:10.1002/jcc.540130812

Description

Wham reweighting algorithm, perhaps used after umbrella sampling.

algorithm md-algorithm

Computer Simulation of Liquids

1989-computer-simulation-of-liquids

M. P. Allen; D. J. Tildesley

1989-01-01 (print)

An efficient newton-like method for molecular mechanics energy minimization of large molecules

1987-minimization

Jay W. Ponder; Frederic M. Richards

1987-10-01 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 8, 7, 1016-1024. doi:10.1002/jcc.540080710

Hydrogen bonding in globular proteins

1984-baker-hubbard

E.N. Baker; R.E. Hubbard

1984-01-01 (print)

Progress in Biophysics and Molecular Biology (Prog. Biophys. Mol. Biol.). 44, 2, 97-179. doi:10.1016/0079-6107(84)90007-5

Description

Hydrogen bond determination

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1983-charmm

Bernard R. Brooks; Robert E. Bruccoleri; Barry D. Olafson; David J. States; S. Swaminathan; Martin Karplus

1983-01-01 (print)

Journal of Computational Chemistry (J. Comput. Chem.). 4, 2, 187-217. doi:10.1002/jcc.540040211

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

1973-shrake-rupley

A. Shrake; J.A. Rupley

1973-09-01 (print)

Journal of Molecular Biology (J. Mol. Biol.). 79, 2, 351-371. doi:10.1016/0022-2836(73)90011-9

Description

Solvation