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

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

doi:10.1021/acs.jpcb.4c04100

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

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

Department of Chemistry

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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	English
Journal	Journal of Physical Chemistry B
Early online date	20 Sep 2024
DOIs	https://doi.org/10.1021/acs.jpcb.4c04100
State	Published - 17 Oct 2024

Bibliographical note

Publisher Copyright:
© 2024 The Authors. Published by American Chemical Society.

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10.1021/acs.jpcb.4c04100

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

@article{19ed75938b294a539404a2a623e9ac96,

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.",

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

note = "Publisher Copyright: {\textcopyright} 2024 The Authors. Published by American Chemical Society.",

year = "2024",

month = oct,

day = "17",

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

language = "אנגלית",

journal = "Journal of Physical Chemistry B",

issn = "1520-6106",

publisher = "American Chemical Society",

}

Hwang, W, Austin, SL, Blondel, A, Boittier, ED, Boresch, S, Buck, M, Buckner, J, Caflisch, A, Chang, HT, Cheng, X, Choi, YK, Chu, JW, Crowley, MF, Cui, Q, Damjanovic, A, Deng, Y, Devereux, M, Ding, X, Feig, MF, Gao, J, Glowacki, DR, Gonzales, JE, Hamaneh, MB, Harder, ED, Hayes, RL, Huang, J, Huang, Y, Hudson, PS, Im, W, Islam, SM, Jiang, W, Jones, MR, Käser, S, Kearns, FL, Kern, NR, Klauda, JB, Lazaridis, T, Lee, J, Lemkul, JA, Liu, X, Luo, Y, MacKerell, AD, Major, DT, Meuwly, M, Nam, K, Nilsson, L, Ovchinnikov, V, Paci, E, Park, S, Pastor, RW, Pittman, AR, Post, CB, Prasad, S, Pu, J, Qi, Y, Rathinavelan, T, Roe, DR, Roux, B, Rowley, CN, Shen, J, Simmonett, AC, Sodt, AJ, Töpfer, K, Upadhyay, M, van der Vaart, A, Vazquez-Salazar, LI, Venable, RM, Warrensford, LC, Woodcock, HL, Wu, Y, Brooks, CL, Brooks, BR & Karplus, M 2024, 'CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed', Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.4c04100

TY - JOUR

T1 - CHARMM at 45

T2 - Enhancements in Accessibility, Functionality, and Speed

AU - Hwang, Wonmuk

AU - Austin, Steven L.

AU - Blondel, Arnaud

AU - Boittier, Eric D.

AU - Boresch, Stefan

AU - Buck, Matthias

AU - Buckner, Joshua

AU - Caflisch, Amedeo

AU - Chang, Hao Ting

AU - Cheng, Xi

AU - Choi, Yeol Kyo

AU - Chu, Jhih Wei

AU - Crowley, Michael F.

AU - Cui, Qiang

AU - Damjanovic, Ana

AU - Deng, Yuqing

AU - Devereux, Mike

AU - Ding, Xinqiang

AU - Feig, Michael F.

AU - Gao, Jiali

AU - Glowacki, David R.

AU - Gonzales, James E.

AU - Hamaneh, Mehdi Bagerhi

AU - Harder, Edward D.

AU - Hayes, Ryan L.

AU - Huang, Jing

AU - Huang, Yandong

AU - Hudson, Phillip S.

AU - Im, Wonpil

AU - Islam, Shahidul M.

AU - Jiang, Wei

AU - Jones, Michael R.

AU - Käser, Silvan

AU - Kearns, Fiona L.

AU - Kern, Nathan R.

AU - Klauda, Jeffery B.

AU - Lazaridis, Themis

AU - Lee, Jinhyuk

AU - Lemkul, Justin A.

AU - Liu, Xiaorong

AU - Luo, Yun

AU - MacKerell, Alexander D.

AU - Major, Dan T.

AU - Meuwly, Markus

AU - Nam, Kwangho

AU - Nilsson, Lennart

AU - Ovchinnikov, Victor

AU - Paci, Emanuele

AU - Park, Soohyung

AU - Pastor, Richard W.

AU - Pittman, Amanda R.

AU - Post, Carol Beth

AU - Prasad, Samarjeet

AU - Pu, Jingzhi

AU - Qi, Yifei

AU - Rathinavelan, Thenmalarchelvi

AU - Roe, Daniel R.

AU - Roux, Benoit

AU - Rowley, Christopher N.

AU - Shen, Jana

AU - Simmonett, Andrew C.

AU - Sodt, Alexander J.

AU - Töpfer, Kai

AU - Upadhyay, Meenu

AU - van der Vaart, Arjan

AU - Vazquez-Salazar, Luis Itza

AU - Venable, Richard M.

AU - Warrensford, Luke C.

AU - Woodcock, H. Lee

AU - Wu, Yujin

AU - Brooks, Charles L.

AU - Brooks, Bernard R.

AU - Karplus, Martin

PY - 2024/10/17

Y1 - 2024/10/17

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.

UR - http://www.scopus.com/inward/record.url?scp=85204702645&partnerID=8YFLogxK

U2 - 10.1021/acs.jpcb.4c04100

DO - 10.1021/acs.jpcb.4c04100

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C2 - 39303207

AN - SCOPUS:85204702645

SN - 1520-6106

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

ER -

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

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