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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CHARMM-GUI Resource Report Resource Website 100+ mentions |
CHARMM-GUI (RRID:SCR_025037) | software resource, web application | Web-based platform to interactively build complex systems and prepare their inputs with well established and reproducible simulation protocols for molecular simulations. | Web-based platform, molecular simulations, |
uses: CHARMM uses: NAMD uses: GROMACS uses: AMBER uses: Desmond uses: OpenMM |
University of Kansas | PMID:18351591 | Free, Freely available | SCR_025037 | 2026-09-05 06:34:48 | 207 | ||||||||
|
GROMACS Resource Report Resource Website 5000+ mentions |
GROMACS (RRID:SCR_014565) | simulation software, software application, software resource, software toolkit | Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers. | simulation, molecular dynamics, software package, software toolkit, biochemical, molecule, protein, lipid, nucleic acid, bond interaction, bio.tools |
is used by: CHARMM-GUI is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ; Nvidia ; Stream Computing Performance Engineers ; Swedish eScience Research Center ; Swedish Foundation for International Cooperation in Research and Higher Education ; Swedish Foundation for Strategic Research ; Swedish National Infrastructure for Computing ; Swedish Research Council |
PMID:26620784 DOI:10.1016/0010-4655(95)00042-E |
Free, Available for download | biotools:gromacs, OMICS_05081 | https://bio.tools/gromacs, https://sources.debian.org/src/gromacs/, https://github.com/gromacs/gromacs | SCR_014565 | Gromacs | 2026-09-05 06:27:48 | 9367 | |||||
|
Desmond Resource Report Resource Website 500+ mentions |
Desmond (RRID:SCR_014575) | simulation software, software application, software resource | Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer. | simulation, supercomputer, commodity cluster, gpu, parallel algorithm, biological system, parallel algorithms, computer, processor | is used by: CHARMM-GUI | Open source, Free for non-commercial use, Commercial entities must contact Schrodinger LLC | SCR_014575 | 2026-09-05 06:27:48 | 946 | ||||||||||
|
AMBER Resource Report Resource Website 1000+ mentions |
AMBER (RRID:SCR_016151) | AMBER | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. | binning, metagenomics, benchmarking, biobox, evaluation, comparison, reconstruction, metric, |
is used by: CHARMM-GUI is listed by: SoftCite |
DOI:10.1101/239582 | Free, Available for download | SCR_016151 | AMBER: Assessment of Metagenome BinnERs | 2026-09-05 06:28:04 | 2205 | |||||||
|
CHARMM Resource Report Resource Website 500+ mentions |
CHARMM (RRID:SCR_014892) | simulation software, software application, software resource | Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools. | visualization, modeling, molecular simulation, materials design, model building tools, analysis, biological systems, peptides, proteins | is used by: CHARMM-GUI | SCR_014892 | 2026-09-05 06:32:59 | 970 | |||||||||||
|
OpenMM Resource Report Resource Website 10+ mentions |
OpenMM (RRID:SCR_000436) | simulation software, software application, software resource, standalone software | Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures. | modeling, molecular dynamics, molecular simulation |
is used by: CHARMM-GUI is listed by: Simtk.org has parent organization: Stanford University; Stanford; California |
NCI P30 CA008748; NIGMS R01 GM062868; NIGMS U54 GM072970 |
PMID:28746339 PMID:23316124 PMID:38154096 DOI:10.1021/acs.jpcb.3c06662 |
Free, Available for download, Freely available | nif-0000-23334 | https://github.com/openmm/openmm, https://openmm.org/, https://openmm.org/documentation, https://github.com/openmm | https://simtk.org/home/openmm | SCR_000436 | OpenMM 8, OpenMM, OpenMM 7, OpenMM 4 | 2026-09-05 06:30:35 | 12 | ||||
|
NAMD Resource Report Resource Website 1000+ mentions |
NAMD (RRID:SCR_014894) | simulation software, software application, software resource, source code | Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. | simulation, molecules, biomolecular systems, visualization | is used by: CHARMM-GUI | PMID:16222654 | Open source | SCR_014894 | 2026-09-05 06:34:00 | 2754 |
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