Molecular modeling of organic and biomolecular systems using BOSS and MCPRO

By W. L. Jorgensen, Julian Tirado-Rives. Journal of Computational Chemistry, 2005

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LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands (2017, methodology): “The core of the LigParGen server is the internal use of the BOSS (32) software to assign the bonded and van der Waals parameters by analogy to the existing atom types in the latest OPLS-AA force field (4).”
Biological and synthetic membranes: What can be learned from a coarse-grained description? (2006, methodology): “Among them are NAMD Molecular Dynamics Software (NAMD) [ 56], the Groningen Machine for Chemical Simulation (GROMACS) [ 57, 58], Groningen Molecular Simulation (GROMOS) [ 59, 60], MDynaMix [ 61], Assisted Model Building with Energy Refinement (AMBER) [ 62], NWChem [ 63, 64], Integrated Model Program”
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances (2014, methodology): “Several methods have been developed to tackle this challenging problem, such as 3D RISM [17-19], SZMAP [20], JAWS [21], WaterMap [18, 22], which are utilized in commercial software [23-25].”
QM/MM Methods for Biological Systems (2006, background): “• MM packages with QM: amber [218, 702], boss (MC simulations, semiempirical QM only) [219, 703], charmm [180, 704] • QM packages with MM: adf [220, 705], gamess-uk [221, 706], Gaussian [707], NWChem [222, 708], QSite/Jaguar [709]; Car–Parrinello MD codes with QM/MM capabilities: cpmd [101, 119, 131”