Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches-Reference-Cited by-同舟云学术

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

Published:2018 Issue:21 Volume:20 Page:14450-14460
ISSN:1463-9076
Container-title:Physical Chemistry Chemical Physics
language:en
Short-container-title:Phys. Chem. Chem. Phys.

Author:

Sun Huiyong¹²³⁴⁵^ORCID,Duan Lili⁶⁷⁸⁴,Chen Fu¹²³⁴,Liu Hui¹²³⁴,Wang Zhe¹²³⁴,Pan Peichen¹²³⁴,Zhu Feng¹²³⁴,Zhang John Z. H.⁶⁷⁸⁴⁹,Hou Tingjun¹²³⁴⁵^ORCID

Affiliation:

1. College of Pharmaceutical Sciences

2. Zhejiang University

3. Hangzhou

4. China

5. State Key Lab of CAD&CG

6. School of Chemistry and Molecular Engineering

7. East China Normal University

8. Shanghai 200062

9. NYU-ECNU Center for Computational Chemistry

Abstract

Nmode entropy and interaction entropy were assessed for MM/PB(GB)SA based on >1500 systems and 6 force fields.

Funder

National Natural Science Foundation of China

China Postdoctoral Science Foundation

Ministry of Science and Technology of the People's Republic of China

Publisher

Royal Society of Chemistry (RSC)

Subject

Physical and Theoretical Chemistry,General Physics and Astronomy

Link

http://pubs.rsc.org/en/content/articlepdf/2018/CP/C7CP07623A

Reference88 articles.

1. Drug–target residence time and its implications for lead optimization

2. The drug–target residence time model: a 10-year retrospective

3. Drug–target residence time: critical information for lead optimization

4. Residence Time of Receptor−Ligand Complexes and Its Effect on Biological Function

5. Characterizing Drug–Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches

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