Protein-ligand interaction energy for crystallographic model building and validation

2016 ◽  
Vol 72 (a1) ◽  
pp. s47-s47
Author(s):  
Daria Beshnova ◽  
Joana Pereira ◽  
Victor Lamzin
Keyword(s):  
Interaction Energy ◽  
Model Building ◽  
Ligand Interaction ◽  
Protein Ligand Interaction

scholarly journals Computational design of novel cyclic urea as HIV-1 protease inhibitor

2007 ◽  
Vol 5 (4) ◽  
pp. 1064-1072 ◽  
Author(s):  
Manga Vijjulatha ◽  
S. Kanth
Keyword(s):  
Biological Activity ◽  
Interaction Energy ◽  
Model Equation ◽  
Computational Design ◽  
Docking Studies ◽  
Computational Techniques ◽  
Ligand Interaction ◽  
Protein Ligand Interaction ◽  
Adme Properties ◽  
Hiv 1

AbstractA series of novel cyclic urea molecules 5,6-dihydroxy-1,3-diazepane-2,4,7-trione as HIV-1 protease inhibitors were designed using computational techniques. The designed molecules were compared with the known cyclic urea molecules by performing docking studies, calculating their ADME (Absorption, Distribution, Metabolism, and Excretion) properties and protein ligand interaction energy. These novel molecules were designed by substituting the P 1/P′ 1 positions (4th and 7th position of 1, 3-diazepan-2-one) with double bonded oxygens. This reduces the molecular weight and increases the bioavailability, indicating better ADME properties. The docking studies showed good binding affinity towards HIV-1 protease. The biological activity of these inhibitors were predicted by a model equation generated by the regression analysis between biological activity (log 1/K i ) of known inhibitors and their protein ligand interaction energy. The synthetic studies are in progress.

scholarly journals On the polarization of ligands by proteins

2020 ◽  
Vol 22 (21) ◽  
pp. 12044-12057
Author(s):  
Soohaeng Yoo Willow ◽  
Bing Xie ◽  
Jason Lawrence ◽  
Robert S. Eisenberg ◽  
David D. L. Minh
Keyword(s):  
Interaction Energy ◽  
Total Protein ◽  
Ligand Interaction ◽  
Polarization Energy ◽  
Core Set ◽  
Protein Ligand Interaction

The ligand polarization energy is evaluated for 286 crystallographic complexes from the PDBBind Core Set. It is found to be a substantial and variable highly fraction of the total protein–ligand interaction energy.

scholarly journals Protein–Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems

2018 ◽  
Vol 122 (32) ◽  
pp. 7821-7827 ◽  
Author(s):  
Gergely Kohut ◽  
Adam Liwo ◽  
Szilvia Bősze ◽  
Tamás Beke-Somfai ◽  
Sergey A. Samsonov
Keyword(s):  
Interaction Energy ◽  
Flexible Systems ◽  
Ligand Interaction ◽  
Protein Ligand Interaction

scholarly journals Estimation of the protein–ligand interaction energy for model building and validation

2017 ◽  
Vol 73 (3) ◽  
pp. 195-202 ◽  
Author(s):  
Daria A. Beshnova ◽  
Joana Pereira ◽  
Victor S. Lamzin
Keyword(s):  
Model Building ◽  
Data Bank ◽  
Binding Mode ◽  
Automated Identification ◽  
Ligand Interaction ◽  
New Approach ◽  
X Ray Crystallography ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Protein Ligand Interaction

Macromolecular X-ray crystallography is one of the main experimental techniques to visualize protein–ligand interactions. The high complexity of the ligand universe, however, has delayed the development of efficient methods for the automated identification, fitting and validation of ligands in their electron-density clusters. The identification and fitting are primarily based on the density itself and do not take into account the protein environment, which is a step that is only taken during the validation of the proposed binding mode. Here, a new approach, based on the estimation of the major energetic terms of protein–ligand interaction, is introduced for the automated identification of crystallographic ligands in the indicated binding site withARP/wARP. The applicability of the method to the validation of protein–ligand models from the Protein Data Bank is demonstrated by the detection of models that are `questionable' and the pinpointing of unfavourable interatomic contacts.

scholarly journals Two Rules on the Protein-Ligand Interaction

2008 ◽  
Author(s):  
Xiaodong Pang ◽  
Linxiang Zhou ◽  
Lily Zhang ◽  
Lina Xu ◽  
Xinyi Zhang
Keyword(s):  
Ligand Interaction ◽  
Protein Ligand Interaction

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

scholarly journals Fragment-centric topographic mapping method guides the understanding of ABCG2-inhibitor interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (14) ◽  
pp. 7757-7766 ◽  
Author(s):  
Yao Wu ◽  
Xin-Ying Gao ◽  
Xin-Hui Chen ◽  
Shao-Long Zhang ◽  
Wen-Juan Wang ◽  
...  
Keyword(s):  
Mapping Method ◽  
Topographic Mapping ◽  
Ligand Interaction ◽  
Mapping Tool ◽  
Protein Ligand Interaction ◽  
Insight Into ◽  
Computational Strategy

Our study gains insight into the development of novel specific ABCG2 inhibitors, and develops a comprehensive computational strategy to understand protein ligand interaction with the help of AlphaSpace, a fragment-centric topographic mapping tool.

Sign in / Sign up

Export Citation Format

Share Document