The role of water molecules in computational drug design
S de Beer, NPE Vermeulen… - Current topics in …, 2010 - ingentaconnect.com
Although water molecules are small and only consist of two different atom types, they play
various roles in cellular systems. This review discusses their influence on the binding …
various roles in cellular systems. This review discusses their influence on the binding …
Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening
The functional characterization of proteins represents a daily challenge for biochemical,
medical and computational sciences. Although finally proved on the bench, the function of a …
medical and computational sciences. Although finally proved on the bench, the function of a …
Rapid context-dependent ligand desolvation in molecular docking
MM Mysinger, BK Shoichet - Journal of chemical information and …, 2010 - ACS Publications
In structure-based screens for new ligands, a molecular docking algorithm must rapidly
score many molecules in multiple configurations, accounting for both the ligand's …
score many molecules in multiple configurations, accounting for both the ligand's …
Fragment-based drug discovery applied to Hsp90. Discovery of two lead series with high ligand efficiency
CW Murray, MG Carr, O Callaghan… - Journal of medicinal …, 2010 - ACS Publications
Inhibitors of the chaperone Hsp90 are potentially useful as chemotherapeutic agents in
cancer. This paper describes an application of fragment screening to Hsp90 using a …
cancer. This paper describes an application of fragment screening to Hsp90 using a …
Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes
Many molecular docking programs are available nowadays, and thus it is of great practical
value to evaluate and compare their performance. We have conducted an extensive …
value to evaluate and compare their performance. We have conducted an extensive …
Estrogen receptor alpha as a key target of red wine polyphenols action on the endothelium
Background A greater reduction in cardiovascular risk and vascular protection associated
with diet rich in polyphenols are generally accepted; however, the molecular targets for …
with diet rich in polyphenols are generally accepted; however, the molecular targets for …
[PDF][PDF] Improved ligand-protein binding affinity predictions using multiple binding modes
E Stjernschantz, C Oostenbrink - Biophysical journal, 2010 - cell.com
Accurate ligand-protein binding affinity prediction, for a set of similar binders, is a major
challenge in the lead optimization stage in drug development. In general, docking and …
challenge in the lead optimization stage in drug development. In general, docking and …
[图书][B] Scientific computing with multicore and accelerators
The hybrid/heterogeneous nature of future microprocessors and large high-performance
computing systems will result in a reliance on two major types of components …
computing systems will result in a reliance on two major types of components …
Role of water in molecular docking simulations of cytochrome P450 2D6
R Santos, J Hritz, C Oostenbrink - Journal of chemical information …, 2010 - ACS Publications
Active-site water molecules form an important component in biological systems, facilitating
promiscuous binding or an increase in specificity and affinity. Taking water molecules into …
promiscuous binding or an increase in specificity and affinity. Taking water molecules into …
Accuracy assessment of protein-based docking programs against RNA targets
Ribonucleic acid (RNA) molecules play central roles in a variety of biological processes and,
hence, are attractive targets for therapeutic intervention. In recent years, molecular docking …
hence, are attractive targets for therapeutic intervention. In recent years, molecular docking …