PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking-Reference-Cited by-同舟云学术

PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

Published:2020-01-15 Issue:6 Volume:124 Page:974-989
ISSN:1520-6106
Container-title:The Journal of Physical Chemistry B
language:en
Short-container-title:J. Phys. Chem. B

Author:

Hwang Sung Bo¹^ORCID,Lee Chang Joon²,Lee Sehan³,Ma Songling⁴,Kang Young-Mook⁵^ORCID,Cho Kwang Hwi⁶,Kim Su-Yeon⁷,Kwon Oh Young⁸,Yoon Chang No⁹,Kang Young Kee¹⁰^ORCID,Yoon Jeong Hyeok¹¹,Nam Ky-Youb¹¹,Kim Seong-Gon¹²,In Youngyong¹³,Chai Han Ha¹⁴,Acree William E.¹⁵^ORCID,Grant J. Andrew¹⁶,Gibson Ken D.¹⁶,Jhon Mu Shik¹⁶,Scheraga Harold A.¹⁶^ORCID,No Kyoung Tai¹¹⁷^ORCID

Affiliation:

1. Yonsei University, Department of Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul KR 120-479, Republic of Korea

2. Dotmatic,Ace Gwanggyo Tower 1, 17 Daehak 4-Ro, Yeongtong-gu, Suwon, Gyeonggido 16226, Republic of Korea

3. Molecular Design Team, New Drug Development Center, Daegu- Gyeongbuk Medical Innovation Foundation (DGMIF), 41061 Daegu City, Republic of Korea

4. Xtalpi-AI Research Center, Xtalpi Inc., 1500-1, Hailong Building Z-Park, Bejing, China 100090

5. Korea Research Institute of Chemical Technology, Drug Information Platform Center, 141, Gajeong-ro, Yuseong-gu, Daejon 34114, Republic of Korea

6. Department of Bioinformatics, Soongsil University, Seoul 156-743, Republic of Korea

7. School of Liberal Arts Education (Chemistry), College of Liberal Arts and Cross-Disciplinary Studies, University of Seoul, Seoul 02504, Republic of Korea

8. Wooreebio Institute, 79 Seonggok-Ro, Danwon-Ku, Ansan-si 15409, Republic of Korea

9. Department of Neuroscience, Korea University of Science and Technology, Seoul 02792, Republic of Korea

10. Department of Chemistry, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk 28644, Republic of Korea

11. Research Center, Pharos I&BT Co., Ltd., 1407 & 1408, 38, Heungan-daero 427beon-gil, Dongan-gu, Anyang 14059, Republic of Korea

12. Korea Biopharm Co., LTD., #C-430 Sigma 2 Office B/D, 164 Tancheonsang-ro, Bundang-gu, Seongnam-si 13631, Republic of Korea

13. Vovi C&E Co. Ltd., 803-ho, 2497, Nambusunhwan-ro, Seocho-gu, Seoul 06724, Republic of Korea

14. National institute of animal science, ReDA, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Republic of Korea

15. Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76230-5017, United States

16. Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States

17. Bioinformatics & Molecular Design Research Center, 50 Yonsei-ro, Seodaemun-gu, Seoul KR 120-479, Republic of Korea

Funder

BMDRC

Publisher

American Chemical Society (ACS)

Subject

Materials Chemistry,Surfaces, Coatings and Films,Physical and Theoretical Chemistry

Link

http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.9b10339

Reference62 articles.

1. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids

2. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids

3. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations

4. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides

5. A New Force Field (ECEPP-05) for Peptides, Proteins, and Organic Molecules

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