E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106662 ◽

2021 ◽

pp. 106662

Author(s):

Ann Brewer ◽

Liqun Zhang

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Lipid Bilayer ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Free Energy Perturbation ◽

Energy Calculation ◽

Energy Perturbation

Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation

Food Science & Nutrition ◽

10.1002/fsn3.2253 ◽

2021 ◽

Author(s):

Ruiyao Chen ◽

Yulu Miao ◽

Xuan Hao ◽

Bei Gao ◽

Mingzhe Ma ◽

...

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Inhibitory Peptides ◽

Ace Inhibitory Peptides ◽

Ace Inhibitory

Protein-Protein Interactions: Interface Analysis, Binding Free Energy Calculation and Interaction Design

Acta Physico-Chimica Sinica ◽

10.3866/pku.whxb20100725 ◽

2010 ◽

Vol 26 (07) ◽

pp. 1988-1997

Author(s):

BAI Hong-Jun ◽

◽

LAI Lu-Hua ◽

◽

...

Keyword(s):

Free Energy ◽

Protein Interactions ◽

Interaction Design ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Protein Protein Interactions ◽

Interface Analysis ◽

Binding Free Energy Calculation of Protein-Carbohydrate Complexes: Learnings so Far

Biophysical Journal ◽

10.1016/j.bpj.2017.11.365 ◽

2018 ◽

Vol 114 (3) ◽

pp. 57a

Author(s):

Sushil K. Mishra ◽

Jaroslav Koča ◽

Yoshiki Yamaguchi

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Insights into the mechanism of inhibition of phospholipase A2 by resveratrol: An extensive molecular dynamics simulation and binding free energy calculation

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107649 ◽

2020 ◽

Vol 100 ◽

pp. 107649

Author(s):

Sajedeh Sharifpour ◽

Sara Fakhraee ◽

Reza Behjatmanesh-Ardakani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Phospholipase A2 ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Mechanism Of Inhibition

Binding Free-Energy Calculation Is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7-Azaindole Derivatives to Glycogen Synthase Kinase-3β

Journal of Chemical Information and Modeling ◽

10.1021/ci400719v ◽

2014 ◽

Vol 54 (6) ◽

pp. 1653-1660 ◽

Cited By ~ 19

Author(s):

Kunihiro Kitamura ◽

Yunoshin Tamura ◽

Tomokazu Ueki ◽

Koji Ogata ◽

Shigeho Noda ◽

...

Keyword(s):

Free Energy ◽

Glycogen Synthase ◽

Binding Free Energy ◽

Glycogen Synthase Kinase ◽

Free Energy Calculation ◽

Energy Calculation ◽

Glycogen Synthase Kinase 3Β ◽

Optimization Calculation ◽

Drug Optimization

Exploring the Interaction of Some N- Benzyloxycarbonyl-L-Phenyl Alanyl-L-Alanine Ketones and Bovine Spleen Cathepsin B by Molecular Modeling and Binding Free Energy Calculation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.1999.10508300 ◽

1999 ◽

Vol 16 (4) ◽

pp. 891-900 ◽

Cited By ~ 3

Author(s):

Indrani Dey

Keyword(s):

Free Energy ◽

Molecular Modeling ◽

Cathepsin B ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model

Bioorganic & Medicinal Chemistry Letters ◽

10.1016/j.bmcl.2007.11.090 ◽

2008 ◽

Vol 18 (2) ◽

pp. 542-545 ◽

Cited By ~ 10

Author(s):

Haizhen Zhong ◽

Karl N. Kirschner ◽

Moses Lee ◽

J. Phillip Bowen

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Partial Charge ◽

Charge Model ◽

Partial Charge Model ◽

Dna Complex

Protein−Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method

Journal of Chemical Information and Modeling ◽

10.1021/ci9002156 ◽

2009 ◽

Vol 49 (8) ◽

pp. 1944-1951 ◽

Cited By ~ 17

Author(s):

Yoshifumi Fukunishi ◽

Daisuke Mitomo ◽

Haruki Nakamura

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Reaction Path ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Path Generation ◽

Faculty Opinions recommendation of End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.736065614.793562721 ◽

2019 ◽

Author(s):

Jeff Wereszczynski

Keyword(s):

Free Energy ◽

Drug Design ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

End Point ◽