Computational Drug Discovery and Design
learning analysis of the most important features for each of the groups of compounds separately, as well as all of the com- poun ...
Kubinyi H, Folkers G, Martin YC (eds) (2006) 3D QSAR in drug design: recent advances. Springer, Berlin Verma J, Khedkar VM, Cou ...
Saeys Y, Inza I, Larran ̃aga P (2007) A review of feature selection techniques in bioinformatics. Bioinformatics 23:2507–2517 R ...
Chapter 17 Computational Exploration of Conformational Transitions in Protein Drug Targets Benjamin P. Cossins, Alastair D. G. L ...
motions have been found to be much conserved in evolution and often repurposed [2, 3]. Proteins also tend to evolve through modu ...
often a layer of subjectivity over whether a region of conformational space is a separate conformation or a part of a larger maj ...
MMC, like MD, is based on statistical physics; but rather than using Newtonian theory to model motions, Monte-Carlo random numbe ...
These atomistic MM models of proteins are, with modern GPU hardware, sufficiently fast to access biologically relevant timescale ...
able to make large ligand displacements and protein collective motions enabling very efficient ligand migration and protein con- ...
predefined collective variables (CVs). However, in contrast, meta- dynamics biases in a history-dependent manner by periodically ...
simulations into one analysis and hence can be easily parallelized across any size of computer resource. MSM analyses of very ra ...
hardware and advanced interprocessor networks [53–55](seeNote 14 ). Published work shows very long timescale simulations and det ...
Currently, the most common application of MD for hidden pockets is the mixed solvent simulations reported in 2009 by a few diffe ...
approaches which drive transitions between crystal structures, but a particularly interesting and automated example, called norm ...
Two-dimensional infrared spectroscopy (2DIR) is another interesting technique able to probe protein secondary structure elements ...
4.3.2 Utilizing Information from Related Proteins Families Another important case is protein conformations which represent an in ...
Without any knowledge of potential hidden conformations, a search with molecular simulation can rely on computational brute forc ...
forward. NMA methods can access many collective motions and has been used in approaches which look for correlated displacements ...
4.4.2 MD Can Offer Detailed Models at Shorter Timescales Despite the difficulty of accessing long timescales, analysis of rela- ...
bridge the gap to longer timescales. Another effective combination is that of SCA analysis and MD [121, 163]. Platforms for anal ...
«
13
14
15
16
17
18
19
20
21
22
»
Free download pdf