Obtaining Binding Free Energy from a Path Sampling without Force Bias

被引:0
|
作者
Duy Phuoc Tran [1 ]
Kitao, Akio [2 ]
机构
[1] Univ Tokyo, Grad Sch Frontier Sci, Dept Computat Biol & Med Sci, Kashiwa, Chiba, Japan
[2] Univ Tokyo, Inst Mol & Cellular Biosci, Tokyo, Japan
关键词
D O I
暂无
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
3168-Pos
引用
收藏
页码:642A / 642A
页数:1
相关论文
共 50 条
  • [31] MSB Estimation of Bound Fraction: Bias from Binding Energy Uncertainty
    Weaver, John B.
    MEDICAL IMAGING 2012: BIOMEDICAL APPLICATIONS IN MOLECULAR, STRUCTURAL, AND FUNCTIONAL IMAGING, 2012, 8317
  • [32] Combined Force-Frequency Sampling for Simulation of Systems Having Rugged Free Energy Landscapes
    Sevgen, Emre
    Guo, Ashley Z.
    Sidky, Hythem
    Whitmer, Jonathan K.
    de Pablo, Juan J.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2020, 16 (03) : 1448 - 1455
  • [33] Free energy profile along a discretized reaction path via the hyperplane constraint force and torque
    Kudin, KN
    Car, R
    JOURNAL OF CHEMICAL PHYSICS, 2005, 122 (11):
  • [34] Predicting binding modes from free energy calculations
    Nervall, Martin
    Hanspers, Peter
    Carlsson, Jens
    Boukharta, Lars
    Aqvist, Johan
    JOURNAL OF MEDICINAL CHEMISTRY, 2008, 51 (09) : 2657 - 2667
  • [35] Comparison of different force field combinations for ligand binding free energy calculations with amber
    Zhang, Han
    Kim, Seonghoon
    Im, Wonpil
    BIOPHYSICAL JOURNAL, 2022, 121 (03) : 49 - 49
  • [36] Entropy effects in hydrocarbon conversion reactions: free-energy integrations and transition-path sampling
    Bucko, T.
    Hafner, J.
    JOURNAL OF PHYSICS-CONDENSED MATTER, 2010, 22 (38)
  • [37] Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange
    Brotzakis, Z. Faidon
    Bolhuis, Peter G.
    JOURNAL OF CHEMICAL PHYSICS, 2019, 151 (17):
  • [38] Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints
    Chen, Po-Chia
    Kuyucak, Serdar
    BIOPHYSICAL JOURNAL, 2011, 100 (10) : 2466 - 2474
  • [39] Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates
    Arasteh, Shima
    Zhang, Bin W.
    Levy, Ronald M.
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2021, 12 (18): : 4368 - 4377
  • [40] Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface
    Hu, Hao
    Lu, Zhenyu
    Parks, Jerry M.
    Burger, Steven K.
    Yang, Weitao
    JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (03):