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    • 18. 发明申请
    • Method of Binding Site and Binding Energy Determination by Mixed Explicit Solvent Simulations
    • 通过混合显式溶剂模拟的结合位点和结合能测定方法
    • US20140358450A1
    • 2014-12-04
    • US14364039
    • 2012-12-20
    • UNIVERSITAT DE BARCELONAINSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS
    • Xavier Barril AlonsoDaniel Alvarez GarciaPeter Schmidtke
    • G06F19/00
    • G16C20/50G16B15/00G16C10/00G16C20/10
    • It is described a method of binding site and binding energy determination by mixed explicit solvent all-atoms molecular dynamics simulations. The macromolecular target for which high affinity binders are sought is simulated in several mixed solvent environments comprising water and at least one amphiphilic organic co-solvent. The simulations are run so that the mixture of solvents are free to react to the presence of the target without the addition of any forces other than those found in the original potential. A correction is applied that helps dissociating the distribution of the different chemical groups found in the amphiphilic organic solvents when calculating their free energies of binding. Additionally, a second correction can be applied accounting for the aggregation of said solvents. The correction helps determining more meaningful absolute, and more accurate relative free energies of binding that can be applied in the rational design of new binders to macromolecular targets.
    • 描述了通过混合显式溶剂全原子分子动力学模拟结合位点和结合能量测定的方法。 在几个包含水和至少一种两亲性有机共溶剂的混合溶剂环境中模拟了寻求高亲和力粘合剂的大分子靶。 运行模拟,使溶剂的混合物自由地与目标物的存在反应,而不添加除原始潜力以外的任何力。 应用校正,当计算其结合的自由能时,有助于解离在两亲性有机溶剂中发现的不同化学基团的分布。 另外,可以应用第二校正来计算所述溶剂的聚集。 该校正有助于确定更有意义的绝对和更准确的结合自由能,可以在新粘合剂对大分子靶标的合理设计中应用。