Computational Drug Discovery and Design
Fig. 2pkCSM web interface. (a) depicts the submission page from pkCSM where users can submit either a single or list of compound ...
predicted value and whether the prediction is numerical, indi- cating the unit of the predicted value, or categorical. A depic- ...
(d) Volume of distribution—The volume of distribution is the theoretical volume that the total dose of a drug would need to be u ...
similarity searches of initial hits using databases of compounds from your commercial suppliers (analoging by cataloging) or lar ...
fluorination and introduction of heteroatoms at potential sites of hydroxylation. Other forms of metabolism to watch out for inc ...
Fig. 3Assessing different aspects that influence protein–ligand affinity. (a) depicts the result page for Arpeggio. A color-code ...
Users have the option to download a Pymol session file to visualize the interactions calculated (seeNote 5). 3.Calculating prote ...
upload a purely textual file, as other formats will now be recognized (e.g., .doc, .xls, and others). If your protein will not ...
Obrezanova O, Csanyi G, Gola JM, Segall MD (2007) Gaussian processes: a method for auto- matic QSAR modeling of ADME properties ...
visualising interatomic interactions in protein structures. J Mol Biol 429(3):365–371 Pires DE, Blundell TL, Ascher DB (2016) m ...
Chapter 15 Protein–Protein Docking in Drug Design and Discovery Agnieszka A. Kaczor, Damian Bartuzi, Tomasz Maciej Ste ̨pniewski ...
design of vaccines or anti-infective drugs. Protein–protein interac- tions are thus responsible for various functions of the cel ...
soluble). Meanwhile, docking of two soluble proteins has to be careful and well validated. Despite these difficulties, protein–p ...
present approaches are able to consider at least protein side-chain flexibility [8]. Flexibility is a critical condition of the ...
Table 1 A summary of global docking programs Software Search algorithm Scoring function Reference (s) ATTRACT Randomized search ...
4 Application of Protein–Protein Docking to Water-Soluble, Membrane-Anchoring, and Integral Membrane Proteins Most protein–prote ...
programs on the protein docking benchmark 4.0. They demon- strated that the docking performance depends on the target and no pro ...
the main players involved in virus entry. Variants of the protein found in various species show different propensity to be targe ...
identified residues were used as docking restraints in HADDOCK. They generated a large initial population of complexes, and 20% ...
above 30% of marketed drugs [53]. Receptors belonging to this class share a common topology of seven transmembrane helixes, conn ...
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