CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Wonmuk Hwang; Steven Austin; Arnaud Blondel; Eric Boittier; Stefan Boresch; Matthias Buck; Joshua Buckner; Amedeo Caflisch; Hao-Ting Chang; Xi Cheng; Yeol Choi; Jhih-Wei Chu; Michael Crowley; Qiang Cui; Ana Damjanovic; Yuqing Deng; Mike Devereux; Xinqiang Ding; Michael Feig; Jiali Gao; David Glowacki; James Gonzales; Mehdi Hamaneh; Edward Harder; Ryan Hayes; Jing Huang; Yandong Huang; Phillip Hudson; Wonpil Im; Shahidul Islam; Wei Jiang; Michael Jones; Silvan Kaser; Fiona Kearns; Nathan Kern; Jeffery Klauda; Themis Lazaridis; Jinhyuk Lee; Justin Lemkul; Xiaorong Liu; Yun Luo; Alexander MacKerell; Dan Major; Markus Meuwly; Kwangho Nam; Lennart Nilsson; Victor Ovchinnikov; Emanuele Paci; Soohyung Park; Richard Pastor; Amanda Pittman; Carol Post; Samarjeet Prasad; Jingzhi Pu; Yifei Qi; Thenmalarchelvi Rathinavelan; Daniel Roe; Benoit Roux; Christopher Rowley; Jana Shen; Andrew Simmonett; Alexander Sodt; Kai Topfer; Meenu Upadhyay; Arjan van der Vaart; Luis Vazquez-Salazar; Richard Venable; Luke Warrensford; H. Woodcock; Yujin Wu; Charles Brooks, III; Bernard Brooks; Martin Karplus

doi:10.1021/acs.jpcb.4c04100

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Wonmuk Hwang
, Steven Austin
, Arnaud Blondel
, Eric Boittier
, Stefan Boresch
, Matthias Buck
, Joshua Buckner
, Amedeo Caflisch
, Hao-Ting Chang
, Xi Cheng
, Yeol Choi
, Jhih-Wei Chu
, Michael Crowley
, Qiang Cui
, Ana Damjanovic
, Yuqing Deng
, Mike Devereux
, Xinqiang Ding
, Michael Feig
, Jiali Gao

David Glowacki, James Gonzales, Mehdi Hamaneh, Edward Harder, Ryan Hayes, Jing Huang, Yandong Huang, Phillip Hudson, Wonpil Im, Shahidul Islam, Wei Jiang, Michael Jones, Silvan Kaser, Fiona Kearns, Nathan Kern, Jeffery Klauda, Themis Lazaridis, Jinhyuk Lee, Justin Lemkul, Xiaorong Liu, Yun Luo, Alexander MacKerell, Dan Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard Pastor, Amanda Pittman, Carol Post, Samarjeet Prasad, Jingzhi Pu, Yifei Qi, Thenmalarchelvi Rathinavelan, Daniel Roe, Benoit Roux, Christopher Rowley, Jana Shen, Andrew Simmonett, Alexander Sodt, Kai Topfer, Meenu Upadhyay, Arjan van der Vaart, Luis Vazquez-Salazar, Richard Venable, Luke Warrensford, H. Woodcock, Yujin Wu, Charles Brooks, III, Bernard Brooks, Martin Karplus

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Abstract

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

Original language	American English
Pages (from-to)	9976-10042
Number of pages	67
Journal	Journal of Physical Chemistry B
Volume	128
Issue number	41
DOIs	https://doi.org/10.1021/acs.jpcb.4c04100
State	Published - 2024

NLR Publication Number

NREL/JA-2800-91515

Keywords

chemical calculations
computer simulations
free energy
interfaces
ligands

Access to Document

10.1021/acs.jpcb.4c04100

Cite this

Hwang, W., Austin, S., Blondel, A., Boittier, E., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., Choi, Y., Chu, J.-W., Crowley, M., Cui, Q., Damjanovic, A., Deng, Y., Devereux, M., Ding, X., Feig, M., ... Karplus, M. (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. Journal of Physical Chemistry B, 128(41), 9976-10042. https://doi.org/10.1021/acs.jpcb.4c04100

@article{7c189bd81af24c5482e9344b51a06757,

title = "CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed",

abstract = "Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.",

keywords = "chemical calculations, computer simulations, free energy, interfaces, ligands",

author = "Wonmuk Hwang and Steven Austin and Arnaud Blondel and Eric Boittier and Stefan Boresch and Matthias Buck and Joshua Buckner and Amedeo Caflisch and Hao-Ting Chang and Xi Cheng and Yeol Choi and Jhih-Wei Chu and Michael Crowley and Qiang Cui and Ana Damjanovic and Yuqing Deng and Mike Devereux and Xinqiang Ding and Michael Feig and Jiali Gao and David Glowacki and James Gonzales and Mehdi Hamaneh and Edward Harder and Ryan Hayes and Jing Huang and Yandong Huang and Phillip Hudson and Wonpil Im and Shahidul Islam and Wei Jiang and Michael Jones and Silvan Kaser and Fiona Kearns and Nathan Kern and Jeffery Klauda and Themis Lazaridis and Jinhyuk Lee and Justin Lemkul and Xiaorong Liu and Yun Luo and Alexander MacKerell and Dan Major and Markus Meuwly and Kwangho Nam and Lennart Nilsson and Victor Ovchinnikov and Emanuele Paci and Soohyung Park and Richard Pastor and Amanda Pittman and Carol Post and Samarjeet Prasad and Jingzhi Pu and Yifei Qi and Thenmalarchelvi Rathinavelan and Daniel Roe and Benoit Roux and Christopher Rowley and Jana Shen and Andrew Simmonett and Alexander Sodt and Kai Topfer and Meenu Upadhyay and \{van der Vaart\}, Arjan and Luis Vazquez-Salazar and Richard Venable and Luke Warrensford and H. Woodcock and Yujin Wu and \{Brooks, III\}, Charles and Bernard Brooks and Martin Karplus",

year = "2024",

doi = "10.1021/acs.jpcb.4c04100",

language = "American English",

volume = "128",

pages = "9976--10042",

journal = "Journal of Physical Chemistry B",

issn = "1520-6106",

publisher = "American Chemical Society",

number = "41",

}

Hwang, W, Austin, S, Blondel, A, Boittier, E, Boresch, S, Buck, M, Buckner, J, Caflisch, A, Chang, H-T, Cheng, X, Choi, Y, Chu, J-W, Crowley, M, Cui, Q, Damjanovic, A, Deng, Y, Devereux, M, Ding, X, Feig, M, Gao, J, Glowacki, D, Gonzales, J, Hamaneh, M, Harder, E, Hayes, R, Huang, J, Huang, Y, Hudson, P, Im, W, Islam, S, Jiang, W, Jones, M, Kaser, S, Kearns, F, Kern, N, Klauda, J, Lazaridis, T, Lee, J, Lemkul, J, Liu, X, Luo, Y, MacKerell, A, Major, D, Meuwly, M, Nam, K, Nilsson, L, Ovchinnikov, V, Paci, E, Park, S, Pastor, R, Pittman, A, Post, C, Prasad, S, Pu, J, Qi, Y, Rathinavelan, T, Roe, D, Roux, B, Rowley, C, Shen, J, Simmonett, A, Sodt, A, Topfer, K, Upadhyay, M, van der Vaart, A, Vazquez-Salazar, L, Venable, R, Warrensford, L, Woodcock, H, Wu, Y, Brooks, III, C, Brooks, B & Karplus, M 2024, 'CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed', Journal of Physical Chemistry B, vol. 128, no. 41, pp. 9976-10042. https://doi.org/10.1021/acs.jpcb.4c04100

TY - JOUR

T1 - CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

AU - Hwang, Wonmuk

AU - Austin, Steven

AU - Blondel, Arnaud

AU - Boittier, Eric

AU - Boresch, Stefan

AU - Buck, Matthias

AU - Buckner, Joshua

AU - Caflisch, Amedeo

AU - Chang, Hao-Ting

AU - Cheng, Xi

AU - Choi, Yeol

AU - Chu, Jhih-Wei

AU - Crowley, Michael

AU - Cui, Qiang

AU - Damjanovic, Ana

AU - Deng, Yuqing

AU - Devereux, Mike

AU - Ding, Xinqiang

AU - Feig, Michael

AU - Gao, Jiali

AU - Glowacki, David

AU - Gonzales, James

AU - Hamaneh, Mehdi

AU - Harder, Edward

AU - Hayes, Ryan

AU - Huang, Jing

AU - Huang, Yandong

AU - Hudson, Phillip

AU - Im, Wonpil

AU - Islam, Shahidul

AU - Jiang, Wei

AU - Jones, Michael

AU - Kaser, Silvan

AU - Kearns, Fiona

AU - Kern, Nathan

AU - Klauda, Jeffery

AU - Lazaridis, Themis

AU - Lee, Jinhyuk

AU - Lemkul, Justin

AU - Liu, Xiaorong

AU - Luo, Yun

AU - MacKerell, Alexander

AU - Major, Dan

AU - Meuwly, Markus

AU - Nam, Kwangho

AU - Nilsson, Lennart

AU - Ovchinnikov, Victor

AU - Paci, Emanuele

AU - Park, Soohyung

AU - Pastor, Richard

AU - Pittman, Amanda

AU - Post, Carol

AU - Prasad, Samarjeet

AU - Pu, Jingzhi

AU - Qi, Yifei

AU - Rathinavelan, Thenmalarchelvi

AU - Roe, Daniel

AU - Roux, Benoit

AU - Rowley, Christopher

AU - Shen, Jana

AU - Simmonett, Andrew

AU - Sodt, Alexander

AU - Topfer, Kai

AU - Upadhyay, Meenu

AU - van der Vaart, Arjan

AU - Vazquez-Salazar, Luis

AU - Venable, Richard

AU - Warrensford, Luke

AU - Woodcock, H.

AU - Wu, Yujin

AU - Brooks, III, Charles

AU - Brooks, Bernard

AU - Karplus, Martin

PY - 2024

Y1 - 2024

N2 - Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

AB - Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

KW - chemical calculations

KW - computer simulations

KW - free energy

KW - interfaces

KW - ligands

U2 - 10.1021/acs.jpcb.4c04100

DO - 10.1021/acs.jpcb.4c04100

M3 - Article

SN - 1520-6106

VL - 128

SP - 9976

EP - 10042

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

IS - 41

ER -

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Abstract

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Keywords

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