Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest ChallengeCitation formats

  • Authors:
  • Hafiz Saqib Ali
  • Arghya Chakravorty
  • Jas Kalayan
  • Samuel De Visser
  • Richard Henchman

Standard

Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge. / Ali, Hafiz Saqib; Chakravorty, Arghya; Kalayan, Jas; De Visser, Samuel; Henchman, Richard.

In: Journal of computer-aided molecular design, 22.06.2021.

Research output: Contribution to journalArticlepeer-review

Harvard

Ali, HS, Chakravorty, A, Kalayan, J, De Visser, S & Henchman, R 2021, 'Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge', Journal of computer-aided molecular design.

APA

Ali, H. S., Chakravorty, A., Kalayan, J., De Visser, S., & Henchman, R. (Accepted/In press). Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge. Journal of computer-aided molecular design.

Vancouver

Ali HS, Chakravorty A, Kalayan J, De Visser S, Henchman R. Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge. Journal of computer-aided molecular design. 2021 Jun 22.

Author

Ali, Hafiz Saqib ; Chakravorty, Arghya ; Kalayan, Jas ; De Visser, Samuel ; Henchman, Richard. / Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge. In: Journal of computer-aided molecular design. 2021.

Bibtex

@article{9792de896ad1495b89e16ca5c8e4d8e3,
title = "Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge",
abstract = "Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy-entropy (EE) method to calculate the host-guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host-guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol-1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.",
author = "Ali, {Hafiz Saqib} and Arghya Chakravorty and Jas Kalayan and {De Visser}, Samuel and Richard Henchman",
year = "2021",
month = jun,
day = "22",
language = "English",
journal = "Journal of computer-aided molecular design",
issn = "1573-4951",
publisher = "Springer Nature",

}

RIS

TY - JOUR

T1 - Energy-Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host-Guest Challenge

AU - Ali, Hafiz Saqib

AU - Chakravorty, Arghya

AU - Kalayan, Jas

AU - De Visser, Samuel

AU - Henchman, Richard

PY - 2021/6/22

Y1 - 2021/6/22

N2 - Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy-entropy (EE) method to calculate the host-guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host-guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol-1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.

AB - Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy-entropy (EE) method to calculate the host-guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host-guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol-1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.

M3 - Article

JO - Journal of computer-aided molecular design

JF - Journal of computer-aided molecular design

SN - 1573-4951

ER -