| 序号 | 专利名 | 申请号 | 申请日 | 公开（公告）号 | 公开（公告）日 | 发明人 |
|---|---|---|---|---|---|---|
| 141 | ANTIBODY LIBRARIES | US13810570 | 2011-07-14 | US20130197201A1 | 2013-08-01 | Maximiliano Vasquez; Arvind Sivasubramanian; Michael Feldhaus |
| The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity. | ||||||
| 142 | Method and/or apparatus for determining codons | US13229228 | 2011-09-09 | US08457903B1 | 2013-06-04 | Robin A. Emig; Richard John Fox; Claes Gustafsson; Sridhar Govindarajan; Jeremy S. Minshull; Guy Cavet |
| Computer processing methods and/or systems for minimizing and/or optimizing data strings in accordance with rules and options. Minimized data strings can represent data sequences important in certain biologic analyses and/or syntheses. In specific embodiments, a request is generated by a user at a client system and received by a server system. The server system accesses initial data indicated or provided by the client system. The server system then performs an analysis to minimize the data needed for further reactions. In specific embodiments, a server can use proprietary methods or data at the server side while protecting those proprietary methods and data from access by the client system. | ||||||
| 143 | UNIVERSAL FIBRONECTIN TYPE III BOTTOM-SIDE BINDING DOMAIN LIBRARIES | US13504824 | 2010-10-27 | US20120208704A1 | 2012-08-16 | Andreas Loew; Brian Edward Vash |
| The invention pertains to a natural-variant combinatorial library of fibronectin Type 3 domain (Fn3) polypeptides useful in screening for the presence of one or more polypeptides having a selected binding or enzymatic activity. The library polypeptides include (a) regions A, AB, B, C, CD, D, E, EF, F, and G having wildtype amino acid sequences of a selected native fibronectin Type 3 polypeptide or polypeptides, and (b) loop regions AB, CD, and EF having selected lengths (Bottom Loops). The Fn3 may also have loop regions BC, DE, and FG having wildtype amino acid sequences, having selected lengths, or mutagenized amino acid sequences (Top Loops). | ||||||
| 144 | Optimization of crossover points for directed evolution | US12557434 | 2009-09-10 | US08108150B2 | 2012-01-31 | Emily C. Mundorff; Sridhar Govindarajan; Claes Gustafsson; Jeremy S. Minshull |
| Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and crossover sites for use in recombination. | ||||||
| 145 | METHODS FOR ARTIFICIAL COMBINATORIAL CONTROL OF BIOLOGICAL SYSTEMS | US13118395 | 2011-05-28 | US20120015834A1 | 2012-01-19 | Giovanni Paternostro; Jacob D. Feala |
| Methods and systems for determining a set of control molecules for use in a combinatorial approach for the treatment of medical conditions, including providing one or more sets of control molecules, where each control molecule within the set acts on a set of targets and the number of control molecules within the one or more sets of control molecules is fewer than the number of targets within the sets of targets; and searching within the sets of control molecules to identify a subset of control molecules that together with a subset of targets form an artificial system to produce a biological effect through the modulation of the subset of targets. | ||||||
| 146 | METHODS, SYSTEMS, AND SOFTWARE FOR IDENTIFYING FUNCTIONAL BIO-MOLECULES | US12979637 | 2010-12-28 | US20110161265A1 | 2011-06-30 | Claes Gustafsson; Sridhar Govindarajan; Robin A. Emig; Richard John Fox; Ajoy K. Roy; Jeremy S. Minshull; S. Christopher Davis; Anthony R. Cox; Phillip A. Patten; Linda A. Castle; Daniel L. Siehl; Rebecca Lynne Gorton; Teddy Chen |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 147 | Methods for identifying and producing polypeptides | US12557463 | 2009-09-10 | US07957912B2 | 2011-06-07 | Sergey A. Selifonov; Willem P. C. Stemmer; Claes Gustafsson; Matthew Tobin; Stephen del Cardayre; Phillip A. Patten; Jeremy Minshull; Lorraine J. Giver |
| In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided. One disclosed method involves identifying and producing a polypeptide. The method may involve (a) receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides; (b) selecting one or more cross-over sites on the sequences thereby defining one or more recombinant polypeptides or recombinant nucleic acids; (c) selecting at least one of the recombinant polypeptides or recombinant nucleic acids; (d) recombining one or more oligonucleotides, at least one of which has a sequence matching some or all of that of the recombinant polypeptides or recombinant nucleic acids selected in (c); (e) selecting at least some of the recombined oligonucleotides produced in (d); and (f) producing a polypeptide encoded by the selected nucleic acid. | ||||||
| 148 | METHOD OF GENERATING AN OPTIMIZED, DIVERSE POPULATION OF VARIANTS | US12867433 | 2009-02-12 | US20110034342A1 | 2011-02-10 | Richard Fox |
| The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides. | ||||||
| 149 | Methods and apparatus for preparing high-dimensional combinatorial experiments | US11348873 | 2006-02-06 | US07882053B2 | 2011-02-01 | Youqi Wang; Marco Falcioni; Stephen J. Turner; C. Eric Ramberg |
| Computer-implemented methods, systems and apparatus, including computer program apparatus, provide techniques for designing a set of experiments to be performed with a set of resources. A plurality of experimental configurations are generated based on a set of parameters describing factors to be varied in the experiments and a set of constraints representing limitations on operations that can be performed with the set of resources. A set of experiments is defined based on a selected configuration. The constraints can be represented as patterns defining an application of a parameter to a set of one or more points of an experimental lattice. | ||||||
| 150 | Methods, systems, and software for identifying functional biomolecules | US11706034 | 2007-02-12 | US07747393B2 | 2010-06-29 | Richard John Fox |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 151 | Methods, systems, and software for identifying functional biomolecules | US10629351 | 2003-07-29 | US07747391B2 | 2010-06-29 | Claes Gustafsson; Sridhar Govindarajan; Robin A. Emig; Richard John Fox; Ajoy K. Roy; Jeremy S. Minshull; S. Christopher Davis; Anthony R. Cox; Phillip A. Patten; Linda A. Castle; Daniel L. Siehl; Rebecca Lynne Gorton; Teddy Chen |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 152 | Methods and systems for generating and evaluating peptides | US11561266 | 2006-11-17 | US07739055B2 | 2010-06-15 | Gregory Stephanopoulos; Kyle Jensen; Christopher Loose |
| Methods to create databases of peptides having a desirable property, such as antimicrobial activity, involving analyzing a database of known peptides for a pattern statistically associated with the desirable property are described herein, The set of sequences being analyzed may include sequences of a desired length containing all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified, the database may be processed in a pattern recognition procedure that identifies a set of patterns that may be representative of a peptide having the desirable property. A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or similarity between one or more of the new sequences and the set of identified patterns. | ||||||
| 153 | Methods for making character strings, polynucleotides and polypeptides having desired characteristics | US11982405 | 2007-10-31 | US20080318795A1 | 2008-12-25 | Sergey A. Selifonov; Willem P.C. Stemmer; Claes Gustafsson; Matthew Tobin; Stephen del Cardayre; Phillip A. Patten; Jeremy Minshull; Lorraine J. Giver |
| In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided. | ||||||
| 154 | Optimization of crossover points for directed evolution | US11818237 | 2007-06-12 | US20080020397A1 | 2008-01-24 | Emily Mundorff; Sridhar Govindarajan; Claes Gustafsson; Jeremy Minshull |
| Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and crossover sites for use in recombination. | ||||||
| 155 | Apparatus and method for designing proteins and protein libraries | US09877695 | 2001-06-08 | US07231328B2 | 2007-06-12 | John R. Desjarlais |
| Methodology for the automated design of proteins is disclosed. Various methods executed by a computer for generating probability matrices, protein sequences, combinatorial libraries of proteins, and optimization of various parameters related to protein design are disclosed. Methodology is applicable to the design and analysis of protein structures and protein sequences. | ||||||
| 156 | Methods, systems, and software for identifying functional biomolecules | US11429628 | 2006-05-05 | US20060205003A1 | 2006-09-14 | Claes Gustafsson; Sridhar Govindarajan; Robin Emig; Richard Fox; Ajoy Roy; Jeremy Minshull; S. Davis; Anthony Cox; Phillip Patten; Linda Castle; Daniel Siehl; Rebecca Gorton; Teddy Chen |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 157 | Methods for making character strings, polynucleotides and polypeptides having desired characteristics | US11339090 | 2006-01-24 | US20060142950A1 | 2006-06-29 | Sergey Selifonov; Willem Stemmer; Claes Gustafsson; Matthew Tobin; Stephen del Cardayre; Phillip Patten; Jeremy Minshull; Lorraine Giver |
| In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided. | ||||||
| 158 | Method, system, and computer program product for analyzing combinatorial libraries | US10058216 | 2002-01-29 | US07054757B2 | 2006-05-30 | Dimitris K Agrafiotis; Victor S Lobanov; Francis R Salemme |
| The invention provides for in silico analysis of a virtual combinatorial library. Mapping coordinates for a training subset of products in the combinatorial library, and features of their building blocks, are obtained. A supervised machine learning approach is used to infer a mapping function ƒ that transforms the building block features for each product in the training subset of products to the corresponding mapping coordinates for each product in the training subset of products. The mapping function ƒ is then encoded in a computer readable medium. The mapping function ƒ can be retrieved and used to generate mapping coordinates for any product in the combinatorial library from the building block features associated with the product. | ||||||
| 159 | Methods for making character strings, polynucleotides and polypeptides having desired characteristics | US09618579 | 2000-07-18 | US07024312B1 | 2006-04-04 | Sergey A. Selifonov; Willem P. C. Stemmer; Claes Gustafsson; Matthew Tobin; Stephen del Cardayre; Phillip A. Patten; Jeremy Minshull; Lorraine J. Giver |
| “In silico” nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided. | ||||||
| 160 | Combinatorial parameter space experiment design | US09840003 | 2001-04-19 | US06983233B1 | 2006-01-03 | Marco Falcioni; C. Eric Ramberg; Youqi Wang |
| Methods and apparatus, including computer program apparatus, implementing techniques for designing sets of combinatorial experiments. A set of experimental parameters, sampling patterns, and constraints defines a set of experiments that is limited to a volume of a hyperspace defined by the set of experimental parameters. Parameters can be grouped by type such that grouped parameters are constrained to perform a common role in the set of experiments. The practicability of the experiment design can be estimated based on the number of experiments in the set of experiments. The experiment design can be used to prepare one or more combinatorial libraries. | ||||||
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