Thông tin chung
  English
  Đề tài NC khoa học
  Bài báo, báo cáo khoa học
  Hướng dẫn Sau đại học
  Sách và giáo trình
  Các học phần và môn giảng dạy
  Giải thưởng khoa học, Phát minh, sáng chế
  Khen thưởng
  Thông tin khác
  Tài liệu tham khảo
  Hiệu chỉnh
 
Số người truy cập: 106,982,674

 Oversampling Free Energy Perturbation Simulation in Determination of the Ligand‐Binding Free Energy
Tác giả hoặc Nhóm tác giả: Son Tung Ngo Trung Hai Nguyen Nguyen Thanh Tung Pham Cam Nam Khanh B. Vu Van V. Vu
Nơi đăng: Journal of Computational Chemistry (John Wiley & Sons, Inc.); Số: 41(7);Từ->đến trang: 611-618;Năm: 2020
Lĩnh vực: Tự nhiên; Loại: Bài báo khoa học; Thể loại: Quốc tế
TÓM TẮT
Determination of the ligand‐binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in …
ABSTRACT
Determination of the ligand‐binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in …
[ https://doi.org/10.1002/jcc.26130 ]
© Đại học Đà Nẵng
 
 
Địa chỉ: 41 Lê Duẩn Thành phố Đà Nẵng
Điện thoại: (84) 0236 3822 041 ; Email: dhdn@ac.udn.vn