BIOINFORMATICS/ MOLECULR MODELING/ DRUG-DESIGN SOFTWARE AVAILABLE IN THE LABORETORY

Software	Brief Discription
ACCELRYS	InsightII
	BIOPOLYMER
	AFFINITY
	LUDI
	LUDI / CAP
	DISCOVER
	Discovery Studios 1.7
TRIPOS	Core Technology:
Teaching	SYBYL
	Biopolymer
	MOLCAD
	Chemical Informatics:
	UNITY Base and UNITY 3D
	Concord Standaline
	Pharmacophore Preparation:
	GALAHAD
	Tuplets
	QSAR:
	QSAR with CoMFA
	Virtual Screening:
	Surflex-Dock
	CScore
	Network License:
	Xtra Net (1-5CPU)
GOLD
OpenEye	Protein and ligand structure:
	WABE: As well as utility with matching electrostatic profiles to other molecules, WABE can find complementary profiles to active sites. WABE generates analogs by a series of isosteric replacements. It is capable of generating anywhere from 10 to 10,000,000 potential leads, depending on the rules of replacement, which are 'learnt' from chemistries presented to it. Because the shape remains the same, the energies of interaction with the residues in an active site can then be calculated very quickly, with full accounting for desolvation effects via the Poisson equation (~100,000 per second). ZAP: Ultimately, one of the hopes for Poisson-Boltzmann technology is to make a contribution to the evaluation of binding energies. To date it has typically been applied naively, i.e. often with poor charge sets, incorrect placements of protons, side chains, incomplete convergence, questionable dielectrics and poor choices of atomic radii. Even so, it often improves trends compared to traditional scoring functions. PB may be limited for binding energies, but the experimental determination has not yet been made. SZYBKI: (It means fast in Polish). We consider the Merck Force Field developed by Halgren et al to still be one of the best force fields available. SZYBKI is our implementation of MMFF, complete with solvent terms for use in ligand, protein-ligand and protein minimizations. AFITT: Our crystallographic project AFITT has, at its heart, the same concepts as the rest of OpenEye tools: that shape, electrostatics and chemistry matter. For instance, many ligand structures deposited in the PDB are manifestly incorrect (over strained, clashing with the protein, in incorrect chemical forms). The goal of AFITT was to give crystallographers and modelers the tools to over come such problems by including a modern forcefield (MMFF), strong cheminformatics (OEChem) and shape fitting for real space refinement. VIDA II: Many of our tools either generate or sift through vast quantities of 3D ligand information, and as such VIDA II is the best program available for large scale visualization. VIDA II can handle small lists of molecules or corporate collections and can view them as multi-pane 3D, 2D depictions, SMILES strings, spreadsheet entries, html forms, graphs and drill-down lists. It can view them in the context of proteins or other small molecules, as simple line models or photo-realistic balls and sticks. With a python core VIDA II is easily scriptable and can be tailored to many end-uses. Works, naturally, on many platforms. FRED: A docking program that fits molecules into the active site of a protein based primarily on shape complementarity. We use Gaussian shape functions to define the interaction of protein and ligand, which gives us a huge advantage in performance. So much so that all poses (rotations and translations) within a given tolerance can be examined in less time than stochastic or rule-based methods (typically, single conformers in milliseconds). Although FRED can use ligand information (allowing constraints to be applied to chemical functionalities), it works primarily as a fast screening tool for Large Scale Virtual Screening. QUACPAC: In addition to providing methods of applying partial charges to proteins, the protein_pka module can estimate both charge states and tautomer preferences both for apo and ligand complexed proteins. Based on the ZAP toolkit, OEChem and MMFF, protein_pka is essential software for correct protein physics.