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Web-based platform to interactively build complex systems and prepare their inputs with well established and reproducible simulation protocols for molecular simulations.
Proper citation: CHARMM-GUI (RRID:SCR_025037) Copy
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.
Proper citation: GROMACS (RRID:SCR_014565) Copy
https://www.deshawresearch.com/resources_desmond.html
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.
Proper citation: Desmond (RRID:SCR_014575) Copy
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.
Proper citation: OpenMM (RRID:SCR_000436) Copy
https://www.charmm.org/charmm/?CFID=66837e22-4ee5-47ba-bcbf-b4b385c2397e&CFTOKEN=0
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.
Proper citation: CHARMM (RRID:SCR_014892) Copy
http://www.ks.uiuc.edu/Research/namd/
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.
Proper citation: NAMD (RRID:SCR_014894) Copy
https://github.com/CAMI-challenge/AMBER
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.
Proper citation: AMBER (RRID:SCR_016151) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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