Docking is a structure-based computational tool that can be used to predict the strength with which a small ligand molecule binds to a macromolecular target. Such binding affinity prediction is crucial to design molecules that bind more tightly to a target and thus are more likely to provide ...
It includes the latest developments in protein-nucleic acid docking algorithms and binding affinity predictions along with a list of computational resources for understanding protein-DNA and protein-RNA interactions. 展开 关键词: Protein-DNA interactions Protein-RNA interactions Three-dimensional structures ...
We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit d...
The electrostatic energy estimated by GB/SA predicted binding affinity (R2 = 17.2 %). However, few Efavirnez analogues showed high binding affinity and activity with RT compared with the co-crystallized compound. This work describes modifications to the X, Y and R substitutes in Efavirenz. 展开...
However, ΔG is made up of two different contributions and many combinations of ΔH and ΔS values can, in principle, elicit the same binding affinity (i.e. the same ΔG and therefore the same Ka). Currently, most molecular or drug design strategies are centered around the optimization of...
In the inference process, we only need to provide docking poses of a pair of structurally similar small molecules to the same protein to obtain the predicted relative binding affinity. A more detailed description of the model framework, and the difference between the Siamese network and traditional...
In this study we have explored other naphthofuran derivatives for their potential to inhibit BACE-1 and GSK-3 through docking, molecular dynamics, binding energy (MM-PBSA). These computational methods were performed to estimate the binding affinity of naphthofuran derivatives towards the BACE-1 and...
Among all proteasomes, the humanoid proteasome showed the highest degree of docking conformation and low inhibition constant (Ki). SAA2 specifically displayed binding to the N-terminal Thr1 residue in the S1 pocket of Mus musculus 5 proteasome along with threonine, lysine and arginine; ...
the heterophily in the protein-ligand complex graph. The second part is the pooling block, which is described in [2] and includes the pairwise interactive pooling (PiPool) for leveraging long-range interactions and the output pooling layer for predicting the protein-ligand binding affinity. ...
The binding affinity from semi-flexible docking (kcal/mol) and the possibility (in parenthesis) of four types of catechins and their chemical groups bindin... BACKGROUND & AIMS: Green tea catechins are known to have anticarcinogenic effects. Epigallocatechin-3-gallate (EGCG) accounts for almost ...