Literature DB >> 26181208

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics.

Jian Yin1, Andrew T Fenley1, Niel M Henriksen1, Michael K Gilson1.   

Abstract

Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by nonoptimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery.

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Year:  2015        PMID: 26181208      PMCID: PMC4664157          DOI: 10.1021/acs.jpcb.5b04262

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  63 in total

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Review 2.  Host-guest chemistry: combinatorial receptors.

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Journal:  J Comput Chem       Date:  2001-11-30       Impact factor: 3.376

4.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

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7.  The particle concept: placing discrete water molecules during protein-ligand docking predictions.

Authors:  M Rarey; B Kramer; T Lengauer
Journal:  Proteins       Date:  1999-01-01

8.  Total chromatographic optical resolutions of alpha-amino acid and ester salts through chiral recognition by a host covalently bound to polystyrene resin.

Authors:  G D Sogah; D J Gram
Journal:  J Am Chem Soc       Date:  1976-05-12       Impact factor: 15.419

9.  Entropy-enthalpy compensation: fact or artifact?

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Journal:  Protein Sci       Date:  2001-03       Impact factor: 6.725

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  13 in total

1.  Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

Authors:  Amanda Li; Michael K Gilson
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

2.  Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.

Authors:  Zhiye Tang; Chia-En A Chang
Journal:  J Chem Theory Comput       Date:  2017-12-14       Impact factor: 6.006

3.  Data-driven analysis of the number of Lennard-Jones types needed in a force field.

Authors:  Michael Schauperl; Sophie Kantonen; Lee-Ping Wang; Michael K Gilson
Journal:  Commun Chem       Date:  2020-11-13

4.  Accounting for apparent deviations between calorimetric and van't Hoff enthalpies.

Authors:  Samuel A Kantonen; Niel M Henriksen; Michael K Gilson
Journal:  Biochim Biophys Acta Gen Subj       Date:  2017-12-06       Impact factor: 3.770

5.  Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Authors:  Andrea Rizzi; Steven Murkli; John N McNeill; Wei Yao; Matthew Sullivan; Michael K Gilson; Michael W Chiu; Lyle Isaacs; Bruce C Gibb; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2018-11-10       Impact factor: 3.686

6.  Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.

Authors:  Jian Yin; Niel M Henriksen; Hari S Muddana; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2018-06-22       Impact factor: 6.006

Review 7.  Predicting Binding Free Energies: Frontiers and Benchmarks.

Authors:  David L Mobley; Michael K Gilson
Journal:  Annu Rev Biophys       Date:  2017-04-07       Impact factor: 12.981

Review 8.  Overview of the SAMPL5 host-guest challenge: Are we doing better?

Authors:  Jian Yin; Niel M Henriksen; David R Slochower; Michael R Shirts; Michael W Chiu; David L Mobley; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2016-09-22       Impact factor: 3.686

9.  HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.

Authors:  Khaleel I Assaf; Mara Florea; Jens Antony; Niel M Henriksen; Jian Yin; Andreas Hansen; Zheng-Wang Qu; Rebecca Sure; Dieter Klapstein; Michael K Gilson; Stefan Grimme; Werner M Nau
Journal:  J Phys Chem B       Date:  2017-12-01       Impact factor: 2.991

10.  DeepBAR: A Fast and Exact Method for Binding Free Energy Computation.

Authors:  Xinqiang Ding; Bin Zhang
Journal:  J Phys Chem Lett       Date:  2021-03-15       Impact factor: 6.475

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