Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

By Junmei Wang, P. Morin, Wei Wang, Peter A. Kollman. Journal of the American Chemical Society, 2001

685 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a5430b24826e8383bbb517da725c3040cdf773c1

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Shengyou Huang
2. Xiaoqin Zou
3. Haim J. Wolfson
4. Ruth Nussinov
5. Peng Sang
6. Xing Du
7. Jing Liang
8. Yi Li

In Infectious Diseases

1. Shengyou Huang
2. Junmei Wang
3. Xiaoqin Zou

In Molecular Biology

1. Shengyou Huang
2. Xiaoqin Zou
3. Ruth Nussinov
4. Haim J. Wolfson
5. Peng Sang
6. Xing Du
7. Jing Liang
8. Yi Li

Citations in the corpus

• Virtual screening strategies in drug discovery: a critical review. (2013, background): “Solvation [73, 74] and entropy [75] contributions can also be considered.”
• Computational approaches in target identification and drug discovery (2016, methodology): “Some examples of the use of suchmethods are the reproduction of binding free energies TIBO derivatives to HIV-1 RT and prediction of the binding mode of efavirenz to HIV-1 RT byMM-PBSA [84], the relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin ”
• Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, background): “The solvent effect can be accounted for either by treating water molecules explicitly or using the implicit (or continuum) solvent models such as Poisson–Boltzmann surface area (PBSA) model [178,179] and the generalized-Born surface area (GBSA) model [180,181].”
• Advances and Challenges in Protein-Ligand Docking (2010, background): “The Poisson-Boltzmann/surface area (PB/SA) models [89–99] and the generalized-Born/surface area (GB/SA) models [100–111] are typical examples of such implicit solvent models.”
• Fast Identification of Possible Drug Treatment of Coronavirus Disease −19 (COVID-19) Through Computational Drug Repurposing Study (2020, methodology): “…energy calculation methods, such as the endpoint MM-PB/GBSA (molecular mechanics-Poisson Boltzmann/ Generalized Born Surface Area) methods 2, 3, 8-21 and the alchemical thermodynamic integration (TI) and free energy perturbation (FEP) methods, 22, 23 have been extensively applied in…”
• Principles of docking: An overview of search algorithms and a guide to scoring functions (2002, methodology): “a reliable index for identifying correct binding modes.(140,148,160,161,227,230)”