Computational Drug Discovery and Design
The archive containing the scripts presented in this chapter is available for download from the following URL:http://cribligand. ...
columns 24–27, instead of columns 23–26. Pymol displays them correctly, but VMD does not. This can be corrected by shifting the ...
(PY) result by the empirical factor of 2, we get consistent and coherent results for the full set of the studied systems. Since ...
dynamics receptor structures in virtual screen- ing. J Chem Inf Model 51:1439–1446 Nichols SE, Riccardo B, McCammon JA (2012) O ...
using enhanced conformational sampling algo- rithms. Biochim Biophys Acta 1858:1635–1651 Arthur EJ, Brooks CL III (2016) Effici ...
Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G (2015) The impact of molecular dynamics on drug design: app ...
Chapter 10 Building Molecular Interaction Networks from Microarray Data for Drug Target Screening Sze Chung Yuen, Hongmei Zhu, a ...
the molecular mechanism of diseases [7, 8]. Identification of dys- regulated genes, i.e., differentially expressed (DE) genes, c ...
Bugliani M, including a total of 13 samples, 7 samples from non-T2DM and 6 samples from T2DM [23]. Also, this microarray dataset ...
3 Methods 3.1 Quality Control All downloaded .CEL files are saved in a single file (e.g., the file can be named by the GEO numbe ...
RNA quality, while the RNA quality from nondiabetic samples is acceptable. It is possible that there is contamination during sam ...
Fig. 4Quality control of arrays. (a) R code for quality control of all arrays. (b) A summary of quality control metrics for all ...
correction [26]. Compared with other processes, the results of different normalization methods are significantly different, and ...
Fig. 5(continued) 186 Sze Chung Yuen et al. ...
Fig. 6Background correction and normalization. (a) R code for background correction and different normali- zation methods of cle ...
The preprocessed data should be stored in an object as soon as the background correction, normalization, probe-specific correc- ...
Fig. 8Group-means parameterization of DE genes. (a) R code for group-means parametrization. (b) R code for group-means parameter ...
data of Entrez IDs, log FCs, and adjustedPvalues to a .txt file named DEgenes. 3.4 Network Analysis Over 300,000 experimentally ...
Fig. 10 Network analysis using InnateDB. (a) Overview of InnateDB. (b) Uploading the genes for constructing network and setting ...
3.6 Correlation Analysis for Each Node in the Module The information of each node is extracted by dividing the column Cross-refe ...
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