Computational Drug Discovery and Design
Newton’s second law of motion. The output is a trajectory which describes the positions and velocities of the particles in the s ...
Refs. [22, 23]). We performed MD simulation using NAMDv2.8 package with the CHARMM22/CMAP biomolecular force-field [24, 25]. The ...
database and hydrophobicity of the protein. The prepared receptor was aligned and oriented to the proper position in the POPC li ...
details, such as formation of unexpected pores in the membrane system, separation of the lipid leaflets, lipid bilayer thickness ...
acidαin the full MSA, which serves as the background frequency. The quantity S¼ P 20 α¼ 1 pi αlogp i α=p α can be regarded as ...
CCðÞ¼v XN i¼ 1 diðÞ;v=ðÞN 1 ! 1 ð 3 Þ whered(i,v) is the minimal number of edges that bridge the nodesiandv. For a given netwo ...
Γξx¼ Cξ Cξx DE Cξ (^) ð 5 Þ where Cξ PN i¼ 1 CξðÞi=N is the average network centrality, and Cξx DE is a value evaluated f ...
conformational ensembles generated from the MD simulated trajectories. CCij¼ hiCBðÞi CBðÞj hiCBðÞi hiCBðÞj ffiffiffiffiffiffif ...
visualized using their pathways. Compared to other existing meth- ods, our approach proved quite powerful in the identification ...
Table 2 List of various enhanced sampling methods in molecular dynamics (MD) simulation Enhanced MD technique Methodology Applic ...
Elastic network model (ENM) is one of the methods which characterize a protein based on its residue interaction network, and EN ...
limitations linked with the identification of specific key residues for protein function. For example, SPM can only identify res ...
Acknowledgments This work was supported by the Mid-career Researcher Program (NRF-2017R1A2B4010084) funded by the Ministry of Sc ...
(13):8637–8641. https://doi.org/10.1073/ pnas.122076099 Kaczor AA, Rutkowska E, Bartuzi D, Targowska-Duda KM, Matosiuk D, Selen ...
kink in transmembrane 6 by a rotamer toggle switch. J Biol Chem 277(43):40989–40996. https://doi.org/10.1074/jbc.M206801200 Trz ...
Chapter 24 Identification of Potential MicroRNA Biomarkers by Meta-analysis Hongmei Zhu and Siu-wai Leung Abstract Meta-analysis ...
Common outcome measures include relative risk, odds ratio, cor- relation coefficient, risk difference, and (standardized) mean d ...
cleavage occurs via the endoribonuclease Dicer to generate the mature miRNAs [17]. Mature miRNAs can associate with one of Argon ...
11–50% of reproducible results [29–31]. We also found that the findings from recent literature reviews on miRNAs were discrepant ...
The process for package installation is shown in Fig.2. The example data as part of a full dataset [7] is used in the statistica ...
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