采用MM/PB(GB)SA方法对常规分子动力学轨迹进行结合自由能计算和能量分解，暂不支持计算熵、不支持膜蛋白。预备知识 MM/PB(GB)SA 计算结合自由能的方法有很多，例如，热力学积分（Thermodynamic Integration，TI）、自由能微扰（Free Energy Perturbation，FEP）、MM/PB(GB)SA、线性相互作用能（Linear Interaction Energ...
通常,MM/PBSA方法(PBTan)比MM/GBSA(GBOBC1)方法表现出更好的排序性能。RESP电荷对MM/PB(GB)SA方法具有最佳性能,而基于AM1-BCC和ESP电荷预测的结果也相当令人满意。 此外,作者还评估了MM/GBSA和MM/PBSA在计算绝对结合自由能的...
但是不清楚这个能量是否准确，MM/PB(GB)SA方法是否能准确的计算金属与小分子配体之间形成的配位键能量...
Cardozo, MM-GB/SA rescoring of docking poses in structure-based lead optimization. J. Chem. Inf. Model. 2008, 48, 958-970.MM-GB/SA rescoring of docking poses in structure-based lead optimization. Guimaraes,C.R. et al. J. Chem. Inf. Model . 2008...
AnaMM/GB/SAS 15-4-9MM-PB(GB)/SAerrormessages ambermd/Questions/mm_pbsa.html#calc_moments_skew2/43 notopened CalcPBSA $AMBERHOME/bin/sander-O-ipbsa_.in-opbsa_. .out-c_.crd.-pnot successful AnaPBSA pbsa_..outnotopened CalcAmber/iAPBS ...
The aim of this research is to understand the source of oseltamivir resistance using MD simulations and the MM/PB(GB)SA binding free energy approaches. Both methods can predict the reduced susceptibility of oseltamivir in good agreement to the IC 50 binding energy, although MM/GBSA underestimates...
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computation Article Prediction of Drug Potencies of BACE1 Inhibitors: A Molecular Dynamics Simulation and MM_GB(PB)SA Scoring Mazen Y. Hamed Chemistry Department, Birzeit University, Birzeit P.O. BOX 14, Palestine; mhamed@birzeit.edu Received: 6 November 2020; Accepted: 7 December 2020; ...
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