ROTATE - Generation of Sets of Diverse Conformations

Overview [hide]

Features & Functionality
User Interface
System Requirements
Additional Info
Evaluation Version

ROTATE generates a diverse and user controlled set of molecular conformations starting from a given 3D model. It provides several methods to the user to fully or partially explore the conformational space in order to influence the number of output conformations while retaining a maximum of structural diversity and ensuring a balanced sampling of the conformational space.

ROTATE has been specifically designed to generate conformations of biological relevance and is robust and powerful enough to process large datasets of chemical structures.

Features & Functionality

Features	Description
Input file formats	SD/RDFile, SYBYL MOL/MOL2, CTX file
Output file formats	SD/RDFile, SYBYL MOL/MOL2, PDB, CTX file
Conformer enumeration	Performs fully automated conformational analysis starting from a single 3D structure Deals with molecules of any size with ring system of any size Adjustable control of energy content of output conformations
Conformational diversity	Removes conformations with atom overlaps or close contacts Removes similar structures based on user-defined similarity threshold
Conformational energy	Generates low-energy conformations Provides user-definable energy threshold for conformation selection
Speed and reliability	Handles a broad range of organic chemistry Processes about 800 small to medium-sized molecules with an average number of 7 rotatable bonds in about 2.5h on a Pentium 4, 2.0 GHz workstation and generates about 125 diverse conformations per molecule