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公开(公告)号：US20060009913A1
公开(公告)日：2006-01-12
申请号：US10901576
申请日：2004-07-29
摘要： The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.
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2.发明申请Systems and methods for predicting the structure and function of multipass transmembrane proteins 审中-公开用于预测多通跨膜蛋白的结构和功能的系统和方法公开(公告)号：US20050136481A1
公开(公告)日：2005-06-23
申请号：US10918531
申请日：2004-08-13
摘要： The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the structure of transmembrane proteins such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a combination of coarse grain sampling methods, such as hydrophobicity analysis, followed by coarse grain molecular dynamics and atomic level molecular dynamics, including accurate continuum solvation. Also included are energy optimization to determine the rotation of helices in the (seven-helical) TM bundle, and optimization of the helix translations along their axes and rotational optimization using hydrophobic moment of the helices, to provide a fast and accurate procedure for predicting GPCR tertiary structure.
摘要翻译： 本发明提供了计算机实现的方法和装置，其使用多尺度分子动力学和分子建模方法来实现分层协议，以预测跨膜蛋白如G-蛋白偶联受体（GPCR）的结构和根据该方案产生的蛋白质结构模型。 该协议具有粗粒度采样方法的组合，如疏水性分析，其次是粗粒分子动力学和原子级分子动力学，包括精确的连续溶剂化。 还包括能量优化以确定（七螺旋）TM束中的螺旋的旋转，以及使用其螺旋的疏水力矩优化沿其轴的螺旋平移和旋转优化，以提供用于预测GPCR的快速和准确的程序 三级结构。
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3.发明申请公开(公告)号：US20070038379A1
公开(公告)日：2007-02-15
申请号：US09816755
申请日：2001-03-23
CPC分类号： G16B15/00
摘要： Computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the structure of transmembrane proteins such as G-Protein Coupled Receptors, and protein structural models generated according to the protocol. The protocol features a combination of coarse grain sampling methods, such as hydrophobicity analysis, followed by coarse grain molecular dynamics and atomic level molecular dynamics, including accurate continuum solvation, to provide a fast and accurate procedure for predicting GPCR tertiary structure.
摘要翻译： 使用多尺度分子动力学和分子模拟方法实现分层协议的计算机实现的方法和装置来预测跨膜蛋白如G-蛋白偶联受体的结构和根据方案产生的蛋白质结构模型。 该协议具有粗粒度采样方法的组合，如疏水性分析，其次是粗粒分子动力学和原子级分子动力学，包括精确的连续溶剂化，为预测GPCR三级结构提供了快速准确的程序。
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4.发明授权System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors 有权用于预测膜蛋白中跨膜结构域的系统和方法，并开采用于识别G蛋白偶联受体的基因组公开(公告)号：US08370074B2
公开(公告)日：2013-02-05
申请号：US12606605
申请日：2009-10-27
摘要： The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.
摘要翻译： 本发明提供计算机实现的方法和装置，其使用多尺度分子动力学和分子模拟方法实现分层协议，以预测蛋白质中的跨膜区域的存在，例如G-蛋白质偶联受体（GPCR），以及根据 协议。 该方案采用粗粒度采样方法，如疏水性分析，为预测跨膜区域提供快速准确的程序。 本发明的方法和装置可用于筛选具有跨膜区的编码蛋白质的蛋白质或多核苷酸数据库，例如GPCR。
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公开(公告)号：US20060121455A1
公开(公告)日：2006-06-08
申请号：US10414452
申请日：2003-04-14
摘要： The instant invention provides methods and implementing computer software for designing mutant proteins (or “Target Protein or TP”) that will preferentially bind one list of prespecified ligands (Active Ligands or AL) with respect to another list of ligands (The Inactive Ligands or IL).
摘要翻译： 本发明提供了用于设计突变蛋白（或“靶蛋白或TP”）的方法并实现计算机软件，该突变蛋白将相对于另一个配体列表优先结合一组预先指定的配体（活性配体或AL）列表（The Inactive Ligands or IL ）。
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