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Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, Im W. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 2017; 38:1114-1124. [PMID: 27862047 PMCID: PMC5403596 DOI: 10.1002/jcc.24660] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 12/16/2022]
Abstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Ave, Argonne, Illinois
| | - Xi Cheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Jumin Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Seonghoon Kim
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Sang-Jun Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Kyu Il Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Hui Sun Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Jeffrey B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland College Park, Maryland
| | - Yifei Qi
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
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Klett J, Núñez-Salgado A, Dos Santos HG, Cortés-Cabrera Á, Perona A, Gil-Redondo R, Abia D, Gago F, Morreale A. MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein–Protein Docking. J Chem Theory Comput 2012; 8:3395-408. [DOI: 10.1021/ct300497z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Javier Klett
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
| | - Alfonso Núñez-Salgado
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
| | - Helena G. Dos Santos
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
| | - Álvaro Cortés-Cabrera
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
- Departamento de Farmacología,
Universidad de Alcalá, Alcalá de Henares, E-28871 Madrid,
Spain
| | - Almudena Perona
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
- SmartLigs Bioinformática
S.L., Fundación Parque Científico de Madrid, c/Faraday,
7. Campus de Cantoblanco UAM, E-28049 Madrid, Spain
| | - Rubén Gil-Redondo
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
- SmartLigs Bioinformática
S.L., Fundación Parque Científico de Madrid, c/Faraday,
7. Campus de Cantoblanco UAM, E-28049 Madrid, Spain
| | - David Abia
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
| | - Federico Gago
- Departamento de Farmacología,
Universidad de Alcalá, Alcalá de Henares, E-28871 Madrid,
Spain
| | - Antonio Morreale
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus
de Cantoblanco UAM, E-28049 Madrid, Spain
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