Role of a reaction coordinate in free energy calculations

2018 ◽  
Vol 44 (13-14) ◽  
pp. 1033-1043 ◽  
Author(s):  
Styliani Consta ◽  
Anatoly Malevanets ◽  
Myong In Oh ◽  
Mahmoud Sharawy
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Reaction Coordinate ◽  
Energy Calculations

scholarly journals On the Role of Dewetting Transitions in Host–Guest Binding Free Energy Calculations

2012 ◽  
Vol 9 (1) ◽  
pp. 46-53 ◽  
Author(s):  
Kathleen E. Rogers ◽  
Juan Manuel Ortiz-Sánchez ◽  
Riccardo Baron ◽  
Mikolai Fajer ◽  
César Augusto F. de Oliveira ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Guest Binding ◽  
Binding Free Energy Calculations

scholarly journals Artificial Reaction Coordinate “Tunneling” In Free Energy Calculations: Nucleic Acid Cleavage By Ribonuclease-H

2009 ◽  
Vol 96 (3) ◽  
pp. 573a
Author(s):  
Edina Rosta ◽  
H. Lee Woodcock ◽  
Bernard R. Brooks ◽  
Gerhard Hummer
Keyword(s):  
Free Energy ◽  
Nucleic Acid ◽  
Free Energy Calculations ◽  
Reaction Coordinate ◽  
Ribonuclease H ◽  
Energy Calculations ◽  
Acid Cleavage

Free energy calculations on binding and catalysis by α-lytic protease: The role of substrate size in the P1 pocket

1991 ◽  
Vol 10 (2) ◽  
pp. 140-148 ◽  
Author(s):  
James W. Caldwell ◽  
David A. Agard ◽  
Peter A. Kollman
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Substrate Size

scholarly journals Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H

2009 ◽  
Vol 30 (11) ◽  
pp. 1634-1641 ◽  
Author(s):  
Edina Rosta ◽  
H. Lee Woodcock ◽  
Bernard R. Brooks ◽  
Gerhard Hummer
Keyword(s):  
Free Energy ◽  
Catalytic Reaction ◽  
Rnase H ◽  
Free Energy Calculations ◽  
Reaction Coordinate ◽  
Energy Calculations

scholarly journals Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations

2020 ◽  
Vol 16 (12) ◽  
pp. 7883-7894
Author(s):  
Ido Y. Ben-Shalom ◽  
Zhixiong Lin ◽  
Brian K. Radak ◽  
Charles Lin ◽  
Woody Sherman ◽  
...  
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Interfacial Water ◽  
Energy Calculations ◽  
Binding Free Energy Calculations

scholarly journals The structure directing role of 1, 3-diaminopropane in the hydrothermal synthesis of iron(III) phosphate

2004 ◽  
Vol 69 (3) ◽  
pp. 179-186 ◽  
Author(s):  
Nevenka Rajic ◽  
Djordje Stojakovic ◽  
Darko Hanzel ◽  
Venceslav Kaucic
Keyword(s):  
Free Energy ◽  
Hydrothermal Synthesis ◽  
Layered Structure ◽  
Lattice Energy ◽  
Iron Phosphate ◽  
Free Energy Calculations ◽  
Hydrothermal Conditions ◽  
Structure Directing Agent ◽  
Energy Calculations

1,3-Diaminopropane (DAP) was used as a structure-directing agent for the hydrothermal synthesis of an organically templated iron phosphate. During crystallization at 180 ?C, iron phosphate (FePO-DAP) with a layered structure was formed after one day. Longer crystallization yielded a mixture of FePO-DAP and leucophosphite, raising the question whether a transformation of FePO-DAP to leucophosphite occurs, or whether DAP decomposes under hydrothermal conditions resulting in leucophosphite formation. Lattice energy and free energy calculations strongly support the supposition that a decomposition of DAP occurs prior to the formation of leucophosphite.

Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations

2009 ◽  
Vol 15 (10) ◽  
pp. 1245-1252 ◽  
Author(s):  
Jianzhong Chen ◽  
Maoyou Yang ◽  
Guodong Hu ◽  
Shuhua Shi ◽  
Changhong Yi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Functional Role ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Dynamics Simulations ◽  
Hiv 1

Automated Assessment of Binding Affinity via Alchemical Free Energy Calculations

2020 ◽  
Author(s):  
Maximilian Kuhn ◽  
Stuart Firth-Clark ◽  
Paolo Tosco ◽  
Antonia S. J. S. Mey ◽  
Mark Mackey ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Free Energy Calculations ◽  
Distinct Advantage ◽  
Binding Affinities ◽  
Structure Based Drug Design ◽  
Energy Calculations ◽  
Kendall’S Τ ◽  
Experimental Values ◽  
Better Than

Free energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented, constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace and OpenMM and uses the AMBER14SB and GAFF2.1 force fields. It was validated on two datasets originally composed by Schrödinger, consisting of 14 protein structures and 220 ligands. Predicted binding affinities were in good agreement with experimental values. For the larger dataset the average correlation coefficient Rp was 0.70 ± 0.05 and average Kendall’s τ was 0.53 ± 0.05 which is broadly comparable to or better than previously reported results using other methods. <br>

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