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3D structure generators for small chemical cmpds

 

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CONFECT Conformations are generated as well as ranked by means of normalized frequency distributions derived from the Cambridge Structural Database (CSD). Following an incremental construction approach, conformations are selected from a systematic enumeration within energetic boundaries. The new tool is benchmarked in several different ways, indicating that it allows the efficient generation of high-quality conformation ensembles. These ensembles are smaller than those produced by state-of-the-art tools, yet they effectively cover conformational space

standalone

Warning the 3D structure of cmpds in CSD can be significantly different from the one of the same cmpd co-crystallized in the presence of a macromolecular partners...

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dataset to test ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. The tool was developped using about 660 PDB files with ligands to test the 3D structure generator. The list of PDB files is in the Supplement of J Chem Inf Modeling (J. Chem. Inf. Model., 2010, 50 (4), pp 534–546) datasets
ALFA It is a fast computational tool for the conformational analysis of small molecules that uses a custom-made iterative algorithm to provide a set of representative conformers in an attempt to reproduce the diversity of states in which small molecules can exist, either isolated in solution or bound to a target. ALFA is distributed free of charge upon request from the authors (see Klett J et al., J Chem Inf Modeling 2014) standalone