Computational Drug Discovery and Design

gain in free energy of binding can be expected if the water in that hydration site is replaced by a ligand. The “occupancy” valu ...

hydration sites that are within the user-specified distance to any of the ligand’s heavy atoms are added up to estimate its prot ...

4 Notes CUDA platform on GPU workstation—This latest version of WATsite relies on OpenMM accelerated MD simulation, but a previ ...

thermodynamics of water molecules. We provide the option for the user to use the Reduce [19] program to adjust the proton- ation ...

Hydration site prediction with and without the presence of bound ligand—The ligand-free (apo) protein structure should be used ...

Li Z, Lazaridis T (2006) Thermodynamics of buried water clusters at a protein-ligand bind- ing interface. J Phys Chem B 110 (3) ...

Chapter 20 Enhanced Molecular Dynamics Methods Applied to Drug Design Projects Sonia Ziada, Abdennour Braka, Julien Diharce, Sam ...

show a remarkable flexibility upon ligand binding, making this simple model inadequate to describe correctly the association and ...

assemblies and transmembrane proteins makes the consideration of the flexibility role more difficult to apprehend. From the theo ...

2.1 Hardware To enhance the computing power, one of the means is to increase the number of central processing units (CPUs) used ...

calculations just like the main CPU on a laptop/desktop but with higher computing performance [22]. The choice of the MD softwar ...

Cap protein termini with ACE and NME residues if the protein is not fully resolved at the extremities (seeNote 1). Then, save t ...

All the simulations were performed using the SHAKE algo- rithm on hydrogen atoms, a 2 fs time step and Langevin dynamics for tem ...

Table 2Description of various molecular dynamics methods: characteristics, limits and applications Linear timedependance? Reacti ...

VrðÞ∗¼V 0 ðÞþr ΔVboostðÞr Depending on the type of the boost potential (ΔVboost(r)), we distinguish three methods of aMD. Boost ...

hEdi) of a precomputed step of equilibration (cMD). From these estimations, we calculate the values ofEthrpandEthrdby adding a q ...

3.4.3 Running the aMD Calculations Once the aMD parameters are defined, we run 200 ns of aMD production with the same conditions ...

Extraction of the principal components of interest: an eigen- value is associated with each eigenvector and the eigenvectors in ...

Analysis From the results of PCA, the conformational sampling is analyzed on a 2D principal component plot as depicted in Fig.2. ...

Here, the first three principal components that accounts for 68.3% of the total variance, as shown on the scree plot, are plotte ...