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1. 发明授权

US09315805B2 Alphabody libraries and methods for producing the same 有权
标题翻译： Alphabody图书馆及其制作方法
公开(公告)号：US09315805B2
公开(公告)日：2016-04-19
申请号：US13994003
申请日：2011-01-06
申请人： Johan Desmet , Ignace Lasters , Maria Henderikx , Anita Wehnert
发明人： Johan Desmet , Ignace Lasters , Maria Henderikx , Anita Wehnert
IPC分类号： C40B50/06 , C12N15/10 , C07K14/00 , C07K16/24 , C07K16/00 , C40B50/12
CPC分类号： C07K16/244 , C07K14/001 , C07K16/00 , C07K16/005 , C07K2317/33 , C07K2318/20 , C12N15/1037 , C12N15/1055 , C40B40/10 , C40B50/12
摘要： The invention provides single-chain Alphabody library comprising at least 100 different-sequence single-chain Alphabody polypeptides, wherein said Alphabody polypeptides differ from each other in at least one of a defined set of 5 to 20 variegated amino acid residue positions, and wherein at least 70% but not all of said variegated amino acid residue positions are located either in the loop, helix surface or linker region of the Alphabody. The invention further provides methods for use of the Alphabody libraries and Alphabodies obtainable by the methods of the invention.
摘要翻译：本发明提供了包含至少100个不同序列单链Alphabody多肽的单链Alphabody文库，其中所述Alphabody多肽在至少一个5至20个杂化氨基酸残基位置中的至少一个中彼此不同，并且其中在至少70％但不是全部所述杂色氨基酸残基位置位于Alphabody的环，螺旋表面或接头区。本发明进一步提供了通过本发明方法可获得的使用阿尔法抗体文库和阿尔培布氏体的方法。

2. 发明申请

US20110137617A1 METHOD FOR GENERATING INFORMATION RELATED TO THE MOLECULAR STRUCTURE OF A BIOMOLECULE 有权
标题翻译：用于产生与生物分子的分子结构相关的信息的方法
公开(公告)号：US20110137617A1
公开(公告)日：2011-06-09
申请号：US12959224
申请日：2010-12-02
申请人： Johan DESMET , Ignace Lasters , Dominique Vlieghe , Carlo Boutton , Philippe Stas , Jan Spriet
发明人： Johan DESMET , Ignace Lasters , Dominique Vlieghe , Carlo Boutton , Philippe Stas , Jan Spriet
IPC分类号： G06F17/50
CPC分类号： G06F19/16 , B01J2219/00689 , B01J2219/00695 , B01J2219/007 , B01J2219/0072 , B01J2219/00722 , B01J2219/00725 , B01J2219/00731 , C07K1/00 , C07K2299/00 , C40B40/06 , C40B40/10 , C40B40/12
摘要： A method for generating information related to the molecular structure of a biomolecule, comprising the steps of: (a) receiving a three-dimensional representation of said molecular structure, comprising a first set of residue portions and a template; and (b) modifying the representation of step (a) by at least one optimization cycle. Each optimization cycle comprises the steps of: (b1) perturbing a first representation of the molecular structure by modifying the structure of one or more of the first set of residue portions; (b2) relaxing the perturbed representation by optimizing the structure of one or more of the non-perturbed residue portions of the first set with respect to the one or more perturbed residue portions; (b3) evaluating the perturbed and relaxed representation of the molecular structure by using an energetic cost function and replacing the first representation by the perturbed and relaxed representation if the latter's global energy is more optimal than that of the first representation; and the method further comprises the steps of (c) terminating the optimization process according to step (b) when a predetermined termination criterion is reached; and (d) outputting to a storage medium or to a consecutive method a data structure comprising information extracted from step (b).
摘要翻译：一种用于产生与生物分子的分子结构相关的信息的方法，包括以下步骤：（a）接收所述分子结构的三维表示，包括第一组残基部分和模板; 和（b）通过至少一个优化周期来修改步骤（a）的表示。每个优化周期包括以下步骤：（b1）通过修改第一组残留部分中的一个或多个的结构扰乱分子结构的第一表示; （b2）通过相对于一个或多个扰动残余部分优化第一组的非扰动残余部分的一个或多个的结构来放松扰动表示; （b3）通过使用能量成本函数来评估分子结构的扰动和松弛表示，并且如果后者的全局能量比第一表示更为优化，则通过扰动和轻松表示来代替第一表示; 并且所述方法还包括以下步骤：（c）当达到预定的终止标准时，终止根据步骤（b）的优化过程; 以及（d）向存储介质或连续方法输出包括从步骤（b）提取的信息的数据结构。

3. 发明授权

US07702465B2 Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom 有权
标题翻译：方法，计算程序，用于预测MHC /肽复合物的性质的装置，以及由其制备的数据和肽
公开(公告)号：US07702465B2
公开(公告)日：2010-04-20
申请号：US10516628
申请日：2003-06-10
申请人： Ignace Lasters , Johan Desmet
发明人： Ignace Lasters , Johan Desmet
IPC分类号： G06F19/00 , C07K14/74 , C07K14/435
CPC分类号： G06F19/16 , G06F19/18
摘要： The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.
摘要翻译：本发明涉及与主要组织相容性（MHC）I类和II类分子复合的肽和肽类似物的基于结构的预测性质的方法。性质主要涉及MHC /肽复合物的三维结构和肽对MHC受体的结合亲和力。本发明还涉及一种计算机程序及其装置。本发明还涉及通过本发明的方法产生的数据。本发明还涉及预期与靶MHC分子结合的肽和肽类似物。因此，本发明涉及免疫学领域，可能应用于疫苗接种的制造，蛋白质的去免疫，以及治疗剂，特别是免疫治疗剂的制造。

4. 发明授权

US08538706B2 Method for affinity scoring of peptide/protein complexes 失效
标题翻译：肽/蛋白复合物的亲和力评分方法
公开(公告)号：US08538706B2
公开(公告)日：2013-09-17
申请号：US13270931
申请日：2011-10-11
申请人： Johan Desmet , Geert Meersseman , Nathalie Boutonnet , Jurgen Pletinckx , Krista De Clercq , Ignace Lasters
发明人： Johan Desmet , Geert Meersseman , Nathalie Boutonnet , Jurgen Pletinckx , Krista De Clercq , Ignace Lasters
IPC分类号： G06F19/16 , G06F19/18
CPC分类号： G06F19/16 , G06F19/18
摘要： The present invention is related to a quantitative structure-based affinity scoring method for peptide/protein complexes. More specifically, the present invention comprises a method that operates on the basis of a highly specific force field function (e.g. CHARMM) that is applied to all-atom structural representations of peptide/receptor complexes. Peptide side-chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. The method of the invention further comprises a de novo approach to estimate dehydration energies from the simulation of individual amino acids in a solvent box filled with explicit water molecules and applying the same force field function as used to evaluate peptide/receptor complex interactions.
摘要翻译：本发明涉及肽/蛋白复合物的基于定量结构的亲和评分方法。更具体地说，本发明包括一种基于应用于肽/受体复合物的全原子结构表示的高度特异性的力场函数（例如CHARMM）来操作的方法。在详细的旋转异构体取样之后进行受控能量细化，对总亲和力的肽侧链贡献进行评分。本发明的方法还包括从填充有显性水分子的溶剂盒中的各个氨基酸的模拟估算脱水能量并应用用于评估肽/受体复合物相互作用的相同的力场函数的从头方法。

5. 发明申请

US20130211808A2 APPARATUS AND METHOD FOR STRUCTURE-BASED PREDICTION OF AMINO ACID SEQUENCES 审中-公开
公开(公告)号：US20130211808A2
公开(公告)日：2013-08-15
申请号：US13472080
申请日：2012-05-15
申请人： Johan DESMET , Ignace LASTERS , Dominique VLIEGHE , Carlo BOUTTON , Philippe STAS
发明人： Johan DESMET , Ignace LASTERS , Dominique VLIEGHE , Carlo BOUTTON , Philippe STAS
IPC分类号： G06F19/16 , G06G7/48
CPC分类号： G06F19/16
摘要： The present invention provides methods and apparatus for analyzing a protein structure.

6. 发明申请

US20120177676A1 ALPHABODIES FOR HIV ENTRY INHIBITION 审中-公开
标题翻译：用于艾滋病毒入侵抑制的字体
公开(公告)号：US20120177676A1
公开(公告)日：2012-07-12
申请号：US13382647
申请日：2010-07-07
申请人： Johan Desmet , Ignace Joseph Isabella Lasters , Sophie Vanwetswinkel
发明人： Johan Desmet , Ignace Joseph Isabella Lasters , Sophie Vanwetswinkel
IPC分类号： A61K39/12 , C12Q1/70 , A61K38/16 , C12N5/10 , C12N15/13 , A61P37/00 , C12N1/19 , C12N1/21 , C07K14/00 , A61P31/18
CPC分类号： C07K14/005 , A61K38/00 , A61K39/00 , C07K16/1063 , C07K2318/20 , C12N2740/16122 , G01N33/56988 , G01N2333/162 , G01N2500/00
摘要： The present invention relates to HIV-1 gp41-binding single-chain 3-stranded alpha-helical coiled coil molecules, denoted “Alphabodies”, nucleic acids encoding said Alphabodies, host cells comprising said nucleic acids, as well as pharmaceutical compositions comprising said Alphabodies, and methods for the treatment, prevention and diagnosis of HIV infection using said Alphabodies.
摘要翻译：本发明涉及表示为“Alphabodies”的编码所述Alphabody的核酸，包含所述核酸的宿主细胞以及包含所述Alphabody的药物组合物的HIV-1 gp41结合单链3链α-螺旋卷曲螺旋分子以及使用所述Alphabody来治疗，预防和诊断HIV感染的方法。

7. 发明申请

US20110245463A1 APPARATUS AND METHOD FOR STRUCTURE-BASED PREDICTION OF AMINO ACID SEQUENCES 审中-公开
标题翻译：用于氨基酸序列的结构预测的装置和方法
公开(公告)号：US20110245463A1
公开(公告)日：2011-10-06
申请号：US13020452
申请日：2011-02-03
申请人： JOHAN DESMET , IGNACE LASTERS , DOMINIQUE VLIEGHE , CARLO BOUTTON , PHILIPPE STAS
发明人： JOHAN DESMET , IGNACE LASTERS , DOMINIQUE VLIEGHE , CARLO BOUTTON , PHILIPPE STAS
IPC分类号： C07K14/00
CPC分类号： G16B15/00
摘要： The present invention provides methods and apparatus for analyzing a protein structure.
摘要翻译：本发明提供了分析蛋白质结构的方法和装置。

8. 发明申请

US20100168398A1 Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom. 审中-公开
标题翻译：方法，计算程序，用于预测MHC /肽复合物的性质的装置，以及由其制备的数据和肽。
公开(公告)号：US20100168398A1
公开(公告)日：2010-07-01
申请号：US12660774
申请日：2010-03-04
申请人： Ignace Lasters , Johan Desmet
发明人： Ignace Lasters , Johan Desmet
IPC分类号： C07K16/00 , C07K14/00 , C07H21/04 , C12P21/06 , G06F17/50 , G06F17/10 , G06N5/04
CPC分类号： G16B15/00 , G16B20/00
摘要： The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The said properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.
摘要翻译：本发明涉及与主要组织相容性（MHC）I类和II类分子复合的肽和肽类似物的基于结构的预测性质的方法。所述性质主要涉及MHC /肽复合物的三维结构和肽对MHC受体的结合亲和力。本发明还涉及一种计算机程序及其装置。本发明还涉及通过本发明的方法产生的数据。本发明还涉及预期与靶MHC分子结合的肽和肽类似物。因此，本发明涉及免疫学领域，可能应用于疫苗接种的制造，蛋白质的去免疫，以及治疗剂，特别是免疫治疗剂的制造。

9. 发明申请

US20060111554A1 Method, computing routine, device for predicting properties of mhc/peptide complexes, and data and peptides produced therefrom 有权
标题翻译：方法，计算程序，用于预测mhc /肽复合物的性质的装置，以及由其制备的数据和肽
公开(公告)号：US20060111554A1
公开(公告)日：2006-05-25
申请号：US10516628
申请日：2003-06-10
申请人： Ignace Lasters , Johan Desmet
发明人： Ignace Lasters , Johan Desmet
IPC分类号： G06F19/00 , C07K14/74
CPC分类号： G06F19/16 , G06F19/18
摘要： The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The said properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.
摘要翻译：本发明涉及与主要组织相容性（MHC）I类和II类分子复合的肽和肽类似物的基于结构的预测性质的方法。所述性质主要涉及MHC /肽复合物的三维结构和肽对MHC受体的结合亲和力。本发明还涉及一种计算机程序及其装置。本发明还涉及通过本发明的方法产生的数据。本发明还涉及预期与靶MHC分子结合的肽和肽类似物。因此，本发明涉及免疫学领域，可能应用于疫苗接种的制造，蛋白质的去免疫，以及治疗剂，特别是免疫治疗剂的制造。

10. 发明申请

US20060093617A1 Peptides for inducing a CTL and/or HTL response to hepatitis C virus 审中-公开
标题翻译：用于诱导丙型肝炎病毒的CTL和/或HTL应答的肽
公开(公告)号：US20060093617A1
公开(公告)日：2006-05-04
申请号：US11140487
申请日：2005-05-31
申请人： Marie-Ange Buyse , Geert Maertens , Erik Depla , Ignace Lasters , Johan Desmet , Denise Baker , Robert Chesnut , Mark Newman , Alessandro Sette , John Sidney , Scott Southwood
发明人： Marie-Ange Buyse , Geert Maertens , Erik Depla , Ignace Lasters , Johan Desmet , Denise Baker , Robert Chesnut , Mark Newman , Alessandro Sette , John Sidney , Scott Southwood
IPC分类号： A61K39/29 , C07K14/18
CPC分类号： C07K14/005 , A61K39/00 , A61K39/12 , A61K39/29 , A61K2039/55566 , A61K2039/57 , C12N2770/24222 , C12N2770/24234
摘要： The present invention is directed to peptides, and nucleic acids encoding them, derived from the Hepatitis C Virus (HCV). The peptides are those which elicit a CTL and/or HTL response in a host. The invention is also directed to compositions and vaccines for prevention and treatment of HCV infection and diagnostic methods for detection of HCV exposure in patients.
摘要翻译：本发明涉及衍生自丙型肝炎病毒（HCV）的肽和编码它们的核酸。肽是在宿主中引起CTL和/或HTL应答的肽。本发明还涉及用于预防和治疗HCV感染的组合物和疫苗以及用于检测患者中HCV暴露的诊断方法。

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