Managing protein flexibility in docking and its applications
β Scribed by Chandrika B-Rao; Jyothi Subramanian; Somesh D. Sharma
- Book ID
- 113568960
- Publisher
- Elsevier Science
- Year
- 2009
- Tongue
- English
- Weight
- 541 KB
- Volume
- 14
- Category
- Article
- ISSN
- 1359-6446
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We have developed a new docking program that explores ligand flexibility. This program can be applied to database searches. The program is similar in concept to earlier efforts, but it has been automated and improved. The algorithm begins by selecting an anchor fragment of a ligand. This fragment is
Flexible database docking with DOCK 4.0 has been evaluated for its ability to retrieve biologically active molecules from a database of approximately 1,000 compounds with known activities against thrombin and the progesterone receptor. The retrieval of known actives and chemically similar but inacti
## Abstract We present a series of molecularβmechanicsβbased protein refinement methods, including two novel ones, applied as part of an induced fit docking procedure. The methods used include minimization; protein and ligand sidechain prediction; a hierarchical ligand placement procedure similar t