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Molecular dynamics (MD) simulations are essential for understanding biomolecular systems but remain challenging to automate.
VMD: visual molecular dynamics
William Humphrey, Andrew Dalke, and Klaus Schulten · 1996
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Molecular dynamics simulations of biomolecules
Martin Karplus and J Andrew McCammon · 2002
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Force fields for protein simulations
Jay W Ponder and David A Case · 2003
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CHARMM: the biomolecular simulation program
Bernard R Brooks, Charles L Brooks III, Alexander D Mackerell Jr, Lennart Nilsson, Robert J Petrella, Benoît Roux, Youngdo Won, Georgios Archontis, Christian Bartels, Stefan Boresch, et al · 2009
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PACKMOL: A package for building initial configurations for molecular dynamics simulations
Leandro Martínez, Ricardo Andrade, Ernesto G Birgin, and José Mario Martínez · 2009
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Gromita: a fully integrated graphical user interface to gromacs 4
Diamantis Sellis, Dimitrios Vlachakis, and Metaxia Vlassi · 2009
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MDAnalysis: a toolkit for the analysis of molecular dynamics simulations
Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, and Oliver Beckstein · 2011
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METAGUI. a VMD interface for analyzing metadynamics and molecular dynamics simulations
Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, and Alessandro Laio · 2012
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MDWiZ: a platform for the automated translation of molecular dynamics simulations
Victor H Rusu, Vitor AC Horta, Bruno AC Horta, Roberto D Lins, and Riccardo Baron · 2014
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MDTraj: A modern open library for the analysis of molecular dynamics trajectories
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, and Vijay S. Pande · 2015
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C Smith, Berk Hess, and Erik Lindahl · 2015
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FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures
Derek Groen, Agastya P. Bhati, James Suter, James Hetherington, Stefan J. Zasada, and Peter V. Coveney · 2016
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, et al · 2017
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MDANSE: An interactive analysis environment for molecular dynamics simulations
G Goret, B Aoun, and Eric Pellegrini · 2017
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PlayMolecule ProteinPrepare: a web application for protein preparation for molecular dynamics simulations
Gerard Martínez-Rosell, Toni Giorgino, and Gianni De Fabritiis · 2017
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Molecular dynamics simulation for all
Scott A Hollingsworth and Ron O Dror · 2018
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QwikMD - gateway for easy simulation with VMD and NAMD
João Vieira Ribeiro, Rafael C Bernardi, Till Rudack, Klaus Schulten, and Emad Tajkhorshid · 2018
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NGLview–interactive molecular graphics for Jupyter notebooks
Hai Nguyen, David A Case, and Alexander S Rose · 2018
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Bringing molecular dynamics simulation data into view
Peter W Hildebrand, Alexander S Rose, and Johanna KS Tiemann · 2019
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Building admiral, an automated molecular dynamics and analysis platform
Matthew P. Baumgartner and Hongzhou Zhang · 2020
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Simulation foundry: Automated and F.A.I.R. molecular modeling
Gudrun Gygli and Juergen Pleiss · 2020
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Molecular architect: A user-friendly workflow for virtual screening
Eduardo H. B. Maia, Lucas Rolim Medaglia, Alisson Marques Da Silva, and Alex G. Taranto · 2020
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ProtoCaller: Robust automation of binding free energy calculations
Miroslav Suruzhon, Tharindu Senapathi, Michael S. Bodnarchuk, Russell Viner, Ian D. Wall, Christopher B. Barnett, Kevin J. Naidoo, and Jonathan W. Essex · 2020
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EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins
Dmitry Suplatov, Yana Sharapova, and Vytas Švedas · 2020
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The protein data bank archive
Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, and John L Markley · 2021
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PyAutoFEP: An automated free energy perturbation workflow for GROMACS integrating enhanced sampling methods
Luan Carvalho Martins, Elio A. Cino, and Rafaela Salgado Ferreira · 2021
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Applications of molecular dynamics simulation in protein study
Siddharth Sinha, Benjamin Tam, and San Ming Wang · 2022
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RadonPy: automated physical property calculation using all-atom classical molecular dynamics simulations for polymer informatics
Yoshihiro Hayashi, Junichiro Shiomi, Junko Morikawa, and Ryo Yoshida · 2022
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AMBER drug discovery boost tools: Automated workflow for production free-energy simulation setup and analysis (professa)
Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J. Giese, and Darrin M. York · 2022
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Voyager: An open-ended embodied agent with large language models
Guanzhi Wang, Yuqi Xie, Yunfan Jiang, Ajay Mandlekar, Chaowei Xiao, Yuke Zhu, Linxi Fan, and Anima Anandkumar · 2023
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Aviary: training language agents on challenging scientific tasks
Siddharth Narayanan, James D Braza, Ryan-Rhys Griffiths, Manu Ponnapati, Albert Bou, Jon Laurent, Ori Kabeli, Geemi Wellawatte, Sam Cox, Samuel G Rodriques, et al · 2024
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Empowering biomedical discovery with AI agents
Shanghua Gao, Ada Fang, Yepeng Huang, Valentina Giunchiglia, Ayush Noori, Jonathan Richard Schwarz, Yasha Ektefaie, Jovana Kondic, and Marinka Zitnik · 2024
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Augmenting large language models with chemistry tools
Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D White, and Philippe Schwaller · 2024
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Automation and machine learning augmented by large language models in catalysis study
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LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in ’t Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, and S. J. Plimpton · 2022
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Language agents achieve superhuman synthesis of scientific knowledge
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