Tripos, Inc

CONCORD TRIPOS, Inc., 1699 South Hanley Road, St. Louis, MO 63144, USA http //www.tripos.com... 

SMS (San Francisco Package of Applications for the Simulation of Molecular Systems). D A Spellmeyer, W C Swope, E-R Evensen, T Cheatham, D M Ferguson and P A KoUman. University of California, San Francisco, USA. d Tripos Inc., 1699 South Hanley Road, St. Louis, Missouri, USA. 

Academic and other nonprofit institutions can get MM3 from qcpe.chem.indiana. edu. The commercial source is Tripos Inc., 1699 South Hanley Road, St. Louis, MO 63144. For resources on MM3 and MM4 see references 1-3 in Langley, C. H. and Allinger, N. L., J. Phys. Chem. 2003, 107, 5208-5216. 

Tripos is a force field created at Tripos Inc. for inclusion in the Alchemy and SYBYL programs. It is sometimes called the SYBYL force field. Tripos is... 

FlexX An extension of the FlexX docking program which increases the efficiency of the docking of combinatorial libraries Tripos, Inc. http //www.tripos.com [32]... 

SYBYL molecular modeling software. Tripos Inc., St Louis, MO, USA, http //WWW. tripos.com. 

A richer fingerprint description is provided by the Daylight [45, 46] or UNITY (Tripos Inc., St. Louis) fingerprints. These incorporate a much broader range of features, notably including connected bond path fragments up to seven bonds long. 

A third and slightly older method available is the UNITY package from Tripos Inc. This also relies on the user to identify pharmacophore features and spatial arrangement. When multiple compounds and biological activity is known, this can be used to focus on a limited number of features or to exclude specific volume from the molecule. The compounds in the database are then compared to the query... 

Chemical Information, Irvine CA Tripos, Inc. St. Louis MO), similarity searching can be carried out around a well-defined compound class using local descriptors such as atom pairs [46, 47] or topomeric shape [48, 49]. Also, ligand-based pharmacophore searches are able to identify follow-up compounds that are less obvious and more diverse than similarity searches [30, 50-54]. The problem with the latter methods is defining the molecular shape or pharmacophore specifically enough to be useful when there are few hits within a compound class and they cannot be reliably aligned (as is often the case for NMR hits in the absence of detailed structural information). 

SemiChem products are available at http //www.semichem.com. AMPAC , available as a stand-alone product with Windows-based and workstation level interfaces, is a semiempirical quantum mechanical program featuring SAMI, AMI, MNDO, MNDO/d, PM3, MNDO/C, MINDO/3 semiempirical methods. AMPAC also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results. The SYBYL/Base program offered by Tripos, Inc. (products described below) provides an interface with interactive graphing and structural display tools that can be used to access AMPAC s calculation tools. 

UNITY Chemical Information Software Version 4.0. Tripos Inc, St. Louis, MO, 1994. 

Suite, [34]), Leadscope Inc. (Leadscope), GoldenHelix Inc. (ChemTree) and Tripos Inc. (SARNavigator). However, there are relatively few papers published in the literature dealing specifically with hit selection schemes, perhaps not surprisingly for a topic that is of immediate interest to pharmaceutical and biotechnology companies rather than academic groups [4, 35, 36]. 

Ho, C.M.W. RACHEL , RACHEL is developed by Drug Design Methodologies LLC, http //www.newdrugdesign.com and is distributed by Tripos Inc, http //www.tripos.com, 2002. 

The precise time to attain equilibrium was not determined but equilibration was monitored both by the drift of total energy and the stability of the system density. The simulation boxes were cubes (for both hexytols) or a truncated octahedron (for MTHP). The VAX 11/750 of the IFLYSIB performed the main calculations. Graphic displays were produced with a personal computer and ALCHEMY software (Tripos Inc., St. Louis). 

We thank the following Novartis Institutes for BioMedical Research for funding JH MDL Information Systems Inc. for the provision of the MDDR database Barnard Chemical Information Ltd., Daylight Chemical Information Systems Inc., the Royal Society, Tripos Inc. and the Wolfson Foundation for software and laboratory support. 

We wish to thank Prof. Tony Rees, Prof. Robert Brasseur, and Dr. Lennart Eriksson for discussion and enthusiastic support. We are very grateful to Prof. Federico Gago (Departemento de Farmacologica, Universidad de Alcala, Madrid, Spain) for providing the HIV data set and thank also Jacques Duret and Tuan Do (Tripos Inc., France) for software support. 

Molecular mechanics models differ both in the number and specific nature of the terms which they incorporate, as well as in the details of their parameterization. Taken together, functional form and parameterization, constitute what is termed a force field. Very simple force fields such as SYBYL, developed by Tripos, Inc., may easily be extended to diverse systems but would not be expected to yield quantitatively accurate results. On the other hand, a more complex force field such as MMFF94 (or more simply MMFF), developed at Merck Pharmaceuticals, while limited in scope to common organic systems and biopolymers, is better able to provide quantitative accounts of molecular geometry and conformation. Both SYBYL and MMFF are incorporated into Spartan. 

SYBYL. A Molecular Mechanics Force Field developed by Tripos, Inc. 

Tripos, Inc. tripos info tripos.com 314-647-1099 St. Louis, Missouri... 

---