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    ALPHABODY LIBRARIES AND METHODS FOR PRODUCING THE SAME
    12.
    发明申请
    ALPHABODY LIBRARIES AND METHODS FOR PRODUCING THE SAME 有权
    ALPHABODY LIBRARIES及其生产方法

    公开(公告)号：US20140066601A1

    公开(公告)日：2014-03-06

    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： C12N15/10 ,  C07K16/00

    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，螺旋表面或连接区中。 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。

    Apparatus and method for structure-based prediction of amino acid sequences
    14.
    发明授权
    Apparatus and method for structure-based prediction of amino acid sequences 有权
    氨基酸序列结构预测的装置和方法

    公开(公告)号：US08229721B1

    公开(公告)日：2012-07-24

    申请号：US10129513

    申请日：2000-11-03

    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： G06G7/48 ,  G01N33/48 ,  G06F19/00

    CPC分类号： G06F19/16

    摘要： The invention provides methods and apparatus for analyzing a protein structure by A) receiving a reference structure (A) forming a three dimensional representation of a protein; B) substituting into the structure of (A) a pattern with amino-acids different from the one of the protein; C) optimizing the conformation of (A) substituted by pattern of (B); D) assessing the energetic compatibility (EC) of the pattern of (B) within the context of the structure of (A) being structurally optimized in (C) with respect to the pattern, by comparing the global energy of the substituted and optimized protein structure with the global energy of the non-substituted reference structure; and E) storing a value reflecting the EC of the pattern together with information related to the structure of the pattern in the form of an energetic compatibility object (ECO).

    摘要翻译： 本发明提供了通过A）接收形成蛋白质的三维表示的参考结构（A）来分析蛋白质结构的方法和装置; B）用不同于蛋白质的氨基酸取代（A）结构的结构; C）优化（A）由（B）的图案取代的构象; D）通过比较取代和优化的蛋白质的全球能量，评估在（A）的结构的上下文中（B）的模式的能量相容性（EC）在（C）中相对于模式在结构上优化 具有非取代参考结构的全球能量结构; 以及E）将反映所述图案的EC的值与能量兼容对象（ECO）形式的与所述图案的结构有关的信息一起存储。

    NON-NATURAL PROTEINACEOUS SCAFFOLD MADE OF THREE NON-COVALENTLY ASSOCIATED PEPTIDES
    15.
    发明申请
    NON-NATURAL PROTEINACEOUS SCAFFOLD MADE OF THREE NON-COVALENTLY ASSOCIATED PEPTIDES 有权
    三非相关肽的非天然蛋白质组蛋白

    公开(公告)号：US20100305304A1

    公开(公告)日：2010-12-02

    申请号：US12676783

    申请日：2008-09-08

    申请人： Johan Desmet ,  Ignace Lasters

    发明人： Johan Desmet ,  Ignace Lasters

    IPC分类号： C07K14/00 ,  C07K1/00

    CPC分类号： C07K1/00 ,  C07K7/08 ,  C07K14/001 ,  C07K2318/20

    摘要： The present invention is related to a non-natural, thermodynamically stable, proteinaceous scaffold consisting of three non-covalently associated peptides, wherein each peptide sequence comprises less than fifty amino acid residues and wherein at least 50% of the said residues are substitutable amino acids into at least ten different amino acid residue types. The present invention is further related to a non-natural, triple-stranded, parallel alpha-helical coiled coil scaffold wherein each of the three constituting peptide sequences comprise between 2 and 7 consecutive heptad repeats, wherein at least 50% of the core residues are isoleucines, wherein all non-core residues are alanines, and wherein the constituting peptide sequences remain associated under physical conditions that are significantly different from physiological conditions.

    摘要翻译： 本发明涉及由三种非共价相关肽组成的非天然的热力学稳定的蛋白质支架，其中每个肽序列包含少于50个氨基酸的残基，并且其中至少50％的所述残基是可取代的氨基酸 至少十种不同的氨基酸残基类型。 本发明进一步涉及非天然的，三链的平行的α-螺旋卷曲的线圈支架，其中三个构成的肽序列中的每一个包含2-7个连续的七重复重复序列，其中至少50％的核心残基是 异亮氨酸，其中所有非核残基是丙氨酸，并且其中构成的肽序列在与生理条件显着不同的物理条件下保持相关。

    Method for Affinity Scoring of Peptide/Protein Complexes
    17.
    发明申请
    Method for Affinity Scoring of Peptide/Protein Complexes 审中-公开
    肽/蛋白复合物的亲和力评分方法

    公开(公告)号：US20080312840A1

    公开(公告)日：2008-12-18

    申请号：US11568108

    申请日：2006-04-21

    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： G01N33/68

    CPC分类号： G16B15/00 ,  G16B20/00

    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。

    METHOD FOR GENERATING INFORMATION RELATED TO THE MOLECULAR STRUCTURE OF A BIOMOLECULE
    19.
    发明申请
    METHOD FOR GENERATING INFORMATION RELATED TO THE MOLECULAR STRUCTURE OF A BIOMOLECULE 有权
    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。

    Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom
    20.
    发明授权
    Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom 有权
    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。