WAbalone (molecular mechanics)
WAscalaph Designer
WAvizo (software)
WAvogadro (software)
WBALL
WChemical Computing Group
WCoNTub
WCoot (software)
WCP2K
WJmol
WKintech Lab
WList of software for nanostructures modeling
WMolden
WMolekel
WNUPACK
WPyMOL
WQuteMol
WRAPTOR (software)
WRasMol
WShelXle
WSpartan (chemistry software)
WUCSF Chimera
WVisual Molecular Dynamics
WYASARA