Chem-X/BASE

Tel. 619-566-1127, fax 619-586-1481, e-mail haney netcom.com Hydropathic INTeraction by empirical calculation of atomistic hydrophobicity of molecules. Grid points based on energetics of hydrophobic and hydrophilic fields can be used for contouring a hydrophobic space and for scoring ligand-macromolecule and macromolecule-macromolecule interactions. Interfaced to SYBYL (CoMFA), Insight II, and Chem-X. Silicon Graphics and Evans 8c Sutherland ESV workstations. 

The use of pharmacophoric descriptors in enhancing the hit-to-lead properties of lead optimization libraries has been described (76). Pharmacophore fingerprints, based on the Chem-X/ChemDiverse multiple pharmacophore descriptors, were used and several issues in the design of lead optimization libraries were addressed. The applicability of... 

The different force fields developed over the years differ considerably with respect to types and number of cross-terms. The TRIPOS, Chem-X, CHARMm, DREIDING, UFF, and COSMIC force fields do not include any cross-terms at all, and accordingly they are all purely diagonal force fields. MM2, the MM2-based force fields, and MMFF93 include a single cross-term (a stretch-bend function), whereas MM3 includes stretch-bend, bend-bend, and torsion-stretch terms. CVFF and CFF91 additionally include stretch-stretch, torsion-bend-bend, and other cross-terms. 

It was found that structures with up to 14 rotatable bonds are readily handled using the rule-based conformational analysis 2 (conjugated and double bonds), 3 (single bonds), and 4 (sp -sp bonds) rotamers per bond were calculated in the databases for such structures. The default for alpha (sp -sp ) bonds in Chem-X is a 6-point analysis, but 4 points can offer a large gain in time without necessarily a reduction in yield. The number of points is based on the increment of rotation about a particular bond and equals 360° per rotational increment. Thus a 60° increment would equal a 6-point bond. For a corporate database of 62,000 company compounds, a total of 29 million conformations were accepted by the rules from a total of 912 million considered... 

Bu X, Base WL, Pirraglia T (1991) Vectorization of the general Monte Carlo classical trajectray program VENUS. J Comput Chem 12 1014-1024... 

Zhang, X.Y., Shah, N.C. and Van Duyne, R.P. (2005) Sensitive and selective chem/biosensing based on surface-enhanced Raman spectroscopy (SERS). Vibrational Spectroscopy, 42,... 

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