Computational Drug Discovery and Design
Chapter 5 De Novo Design of Ligands Using Computational Methods Venkatesan Suryanarayanan, Umesh Panwar, Ishwar Chandra, and San ...
hypotheses but also enables to secure intellectual property rights and in the identification of new molecules significantly elic ...
matching the interaction sites are grown and linked based on the connecting rules. Predicted ligands are ranked by estimated bin ...
Chemically advanced template search (CATS) for scaffold hopping. AutoDock Vina 1.1.2 for molecular docking. Gromacs 4.5.5 to st ...
Table 1 Examples of various generated compounds through de novo design approaches S. No. Structure of compound Target Software u ...
Table 1 (continued) S. No. Structure of compound Target Software used Reference 7 HDAC inhibitors PhDD (Pharmacophore- based de ...
Table 1 (continued) S. No. Structure of compound Target Software used Reference 13 PPARαagonist SQUIRREL (sophisticated QUantifi ...
Table 2 List of De novo design software or programs. S. No. De novo design software or program Year of publication Concept of fu ...
Table 2 (continued) S. No. De novo design software or program Year of publication Concept of function Receptor (R)/Ligand (L) ba ...
empirical scoring function (SCORE 2.0) [80] and bioavailability by a set of chemical rules with parameters: molecular weight, lo ...
Targeted protein’s preprocessing and refinement can be per- form by other tools like Schrodinger Protein preparation wiz- ard ( ...
(No. DST/INSPIRE Fellowship/2012/482) and Alagappa Uni- versity for AURF (No. Ph.D./1122/AURF FELLOWSHIP/ 2015) respectively. Re ...
design, synthesis, and evaluation of novel nonsteroidal phenanthrene ligands for the estrogen receptor. J Med Chem 46:1408–1418 ...
Gillett VJ, Myatt G, Zsoldos Z, Johnson AP (1995) SPROUT, HIPPO and CAESA: tools for de novo structure generation and estima- t ...
Fechner U, Schneider G (2007) Flux (2): comparison of molecular mutation and cross- over operators for ligand-based de novo des ...
Mombelli E (2008) An evaluation of the pre- dictive ability of the QSAR software packages, DEREK, HAZARDEXPERT and TOPKAT, to d ...
Chapter 6 Molecular Dynamics Simulation and Prediction of Druggable Binding Sites Tianhua Feng and Khaled Barakat Abstract Bindi ...
methods are becoming more promising in this aspect. These computational methods are usually composed of two subsequent stages, n ...
simulations [22]. The snapshots extracted from the MD trajectory represent multiple conformers of the protein structure, involvi ...
residue properties for PPIs, and used this information to guide their search for binding sites in heterodimer complexes [30]. Th ...
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