Computational Drug Discovery and Design
hydrophobicity and hydrogen bond capacities, allowing them to interact with many parts on the protein surface. A fast Fourier tr ...
Most of the current methods search for a binding site using a static protein structure and the calculated values of the various ...
A more complicated example is the discovery of a hidden trench in HIV integrase, which is not accessible within the available cr ...
The generation of a conformational ensemble involves two steps. First is to run an MD simulation on the target structure to gene ...
the protein structure is soaked in different concentrations of differ- ent explicit solvents, allowing these solvent molecules t ...
from these interactions [35]. The maximum binding affinity can be obtained by calculating the associated free energy,ΔGi. It cou ...
shock protein 90 N-terminal domain (Hsp90) and the HIV-1 protease (HIVpr). MDmix method showed more accurate interac- tion map a ...
with Tamiflu and mutations at the binding site can cause resistance against the drug. Therefore, enhancing drug selectivity and ...
3.3 A Cryptic Site Problem: Bcl-xL Protein As discussed above, a cryptic site is defined as a hidden binding site when the prote ...
protein; however, they indirectly influence the activity by inducing conformational changes within the protein structure. Identi ...
Theoretically, multiple short MD simulations are better than one extensive MD simulation. This is mainly because multiple MD si ...
Ganesan A, Coote ML, Barakat K (2017) Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov To ...
Ortiz-Sanchez JM, Nichols SE, Sayyah J, Brown JH, McCammon JA, Grant BJ (2012) Identification of potential small molecule bind- ...
Chapter 7 Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein–Ligand Docking Method Woong-Hee Shin ...
structure of a target receptor protein and compute complementa- rities between the ligand binding pocket of the receptor and lig ...
of coefficients from a series expansion of the 3D function into 3D Zernike basis function [14]. Our group has applied 3DZD to so ...
run PL-PatchSurfer2, andexampleprovides a step-by-step example of a virtual screening process. The details of the required progr ...
APBS and PDB2PQR: APBS [19] calculates molecular surface and the electrostatic potential on molecular surface by solving the Poi ...
[PDB file] is a name of PDB file that has a receptor and a ligand structure. [Chain ID] should be matched to a chain name in PDB ...
ligand, such as a computationally modeled structure or an apo structure, the user can provide a potential bound ligand from a ho ...
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