Protein modeling Tripos

Some of the more approximate or specialized FFs encountered in the literature include CFF, CHEM-X, COSMIC, CYFF, DREIDING, MMX, SHAPES, TRIPOS, VALBOND, and UFF. Well-known FFs for modeling proteins and nucleic acids include AMBER, CHARMM, ECEPP, GROMOS, OPLS and their variants. Some of these latter FFs compromise the quality of reproducing subtle intramolecular electronic effects for the sake of being fast enough to treat biomacromolecules in long molecular simulations. 

Sybyl Program with modules for homology modeling, protein structure analysis, pharmacophore/3D-QSAR modeling, MD, automated docking www.tripos.com/sciTech/inSilicoDisc/ moleculeModeling/sybyl.html... 

As a logical consequence, these methods were introduced in QSAR analyses and a new discipline, 3D QSAR, was bom. The major breakthrough in this field was achieved by Cramer et al.f who in 1988 described the application of comparative molecular field analysis (CoMFA) for the evaluation of the binding properties of steroids to carrier proteins. This approach, for which interestingly a patent application was filed by Cramer and Wold, and assigned to the software company Tripos, was based primarily on the previous work of Wise et on a dynamic lattice-oriented molecular modeling system (DYLOMMS) dating... 

---