CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs Article Swipe
Kye Won Wang
,
Jumin Lee
,
Han Zhang
,
Donghyuk Suh
,
Wonpil Im
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jpcb.2c05294
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jpcb.2c05294
Implicit solvent models are widely used because they are advantageous to speed up simulations by drastically decreasing the number of solvent degrees of freedom, which allows one to achieve long simulation time scales for large system sizes. CHARMM-GUI, a web-based platform, has been developed to support the setup of complex multicomponent molecular systems and prepare input files. This study describes an Implicit Solvent Modeler (ISM) in CHARMM-GUI for various generalized Born (GB) implicit solvent simulations in different molecular dynamics programs such as AMBER, CHARMM, GENESIS, NAMD, OpenMM, and Tinker. The GB models available in ISM include GB-HCT, GB-OBC, GB-neck, GBMV, and GBSW with the CHARMM and Amber force fields for protein, DNA, RNA, glycan, and ligand systems. Using the system and input files generated by ISM, implicit solvent simulations of protein, DNA, and RNA systems produce similar results for different simulation packages with the same input information. Protein-ligand systems are also considered to further validate the systems and input files generated by ISM. Simple ligand root-mean-square deviation (RMSD) and molecular mechanics generalized Born surface area (MM/GBSA) calculations show that the performance of implicit simulations is better than docking and can be used for early stage ligand screening. These reasonable results indicate that ISM is a useful and reliable tool to provide various implicit solvent simulation applications.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.jpcb.2c05294
- OA Status
- green
- Cited By
- 14
- References
- 91
- Related Works
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- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4296327630Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1021/acs.jpcb.2c05294Digital Object Identifier
- Title
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CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation ProgramsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-09-19Full publication date if available
- Authors
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Kye Won Wang, Jumin Lee, Han Zhang, Donghyuk Suh, Wonpil ImList of authors in order
- Landing page
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https://doi.org/10.1021/acs.jpcb.2c05294Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.ncbi.nlm.nih.gov/pmc/articles/9551160Direct OA link when available
- Concepts
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Molecular dynamics, Computer science, Solvent models, Computational science, Solvent, Computational chemistry, Chemistry, Solvation, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
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14Total citation count in OpenAlex
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2025: 5, 2024: 7, 2023: 2Per-year citation counts (last 5 years)
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91Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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