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OS: Linux

WHAT IF is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.

WHAT IF is a computer program used in a wide variety of in silico macromolecular structure research fields such as:

Homology models of protein tertiary structures as well as quaternary structures,
Validation of protein structures, noticeably those deposited in the PDB
Correction of protein structures
Visualisation of macromolecules and their interaction partners (lipids, drugs, ions, water).
Interactive manipulation of macromolecules

Link: http://swift.cmbi.kun.nl/whatif/