SwissParam: A fast force field generation tool for small organic molecules

By Vincent Zoete, M. Cuendet, Aurélien Grosdidier, Olivier Michielin. 2011

2,144 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands (2017, methodology): “The SwissParam (23) server produces CHARMM input files combining bonded parameters from MMFF and nonbonded ones from CHARMM22.”
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina (2024, background): “…two different scoring functions: (i) the AC docking score, which consists of the CHARMM force field energy plus the FACTS solvation energy terms ( 33–35 ), and (ii) the SwissParam score, which provides an estimate of the binding free energy as a weighted sum of the polar and nonpolar terms ( 36 ).”
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules (2019, methodology): “Apart from regular updates, other in-house tools (such as SwissDock (16), Swiss-Param (17) or SwissBioisostere (19)) will be further connected in order to propose, ultimately, a fully integrated web-based drug design environment.”
Probing Solvent–Ligand Interactions in Colloidal Nanocrystals by the NMR Line Broadening (2018, methodology): “interactions of the MEEAA ligands and solvent molecules were obtained from the SwissParam force field generation tool.(52) The cell size of the simulations were determined through an initial simulation run of 100 ps in the NPT ensemble with a variable cell volume.”
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies (2014, positive): “Programs and web-servers that can be used to obtain parameters suitable for both atomistic simulations and computational drug design include: Antechamber which can provide parameters compatible with the Generalized Amber Force Feld (GAFF) [4, 5]; the YASARA AutoSMILES server [6] which also generates”
SwissDock, a protein-small molecule docking web service based on EADock DSS (2011, methodology): “First, manually curated protein structures can be downloaded from the web site, and original PDB files can be prepared through ad hoc scripts (19,20).”