公开(公告)号：WO2017072794A1

公开(公告)日：2017-05-04

申请号：PCT/IN2016/050367

申请日：2016-10-28

Applicant: COUNCIL OF SCIENTIFIC AND INDUSTRIAL RESEARCH

Inventor： KARTHIKEYAN, Muthukumarasamy ,  VYAS, Renu

IPC: G06F19/00 ,  G06F19/16 ,  G06F9/48 ,  G06F9/54 ,  G06F9/445

CPC classification number: G06F9/4843 ,  G06F9/445 ,  G06F9/54 ,  G06F19/16 ,  G06F19/70 ,  G06F19/706 ,  G06F19/709

Abstract: An automated method for remote computing of molecular docking & dynamics from one or more jobs in a network of plurality of users is disclosed herein. The invention additionally employs a system to execute the said method comprising at least one user device, a remote computing server and a remote database. The job defining action tags are received and scanned by the remote server. A semantic analysis is performed on the jobs to distinguish between customized and non-customized tasks. A data analysis of the said jobs is packaged in a compressed format. The user is continually updated of the job status. A public link is generated and sent to the user to download the results. The link is disabled after the downloading of the results to ensure the security of the data. The method avoids any duplication of jobs and can be performed even when the user is offline.

Abstract translation:

一种用于远程计算分子对接和放大的自动化方法。 本文公开了来自多个用户的网络中的一个或多个作业的动态。 本发明另外采用一种系统来执行所述方法，该系统包括至少一个用户设备，远程计算服务器和远程数据库。 作业定义动作标签由远程服务器接收和扫描。 对作业执行语义分析以区分定制和非定制任务。 所述作业的数据分析以压缩格式打包。 用户不断更新作业状态。 生成公共链接并发送给用户以下载结果。 下载结果后链接被禁用以确保数据的安全性。 该方法避免了作业的重复，甚至可以在用户离线时执行。

公开(公告)号：WO2016077823A3

公开(公告)日：2016-10-06

申请号：PCT/US2015060863

申请日：2015-11-16

Applicant: D E SHAW RES LLC

Inventor： TANG PING TAK PETER ,  GROSSMAN J P ,  BATSON BRANNON ,  DROR RON

IPC: G06F19/00

CPC classification number: G06F19/701 ,  G06F19/709

Abstract: A method comprising causing a computer to determine that a topological distance between two particles is less than a threshold.

Abstract translation: 一种方法，包括使计算机确定两个粒子之间的拓扑距离小于阈值。

公开(公告)号：WO2015168295A1

公开(公告)日：2015-11-05

申请号：PCT/US2015/028309

申请日：2015-04-29

Applicant: SCHRODINGER, INC.

Inventor： BECKER, Scott ,  SCHOOLMAN, Brian ,  JORDAN, William, C. ,  MURCKO, Mark ,  FRIESNER, Richard

IPC: G06Q10/00

CPC classification number: G06F19/709 ,  G06F17/30011 ,  G06F19/705 ,  G06F19/706

Abstract: Methods and systems for drug discovery collaboration provide collaborative drug discovery electronic workplaces simultaneously accessible by multiple user computing devices. In certain embodiments, a server computer running a server side application communicates with multiple user computing devices. The server side application communicates with electronic databases that define the parameters of each electronic workplace. Each workplace includes an indication of one or more items, such as compounds, and data pertaining to such items, such as computational and experimental data. Updates to a workplace made by one user may be saved to the workplace definition and propagated and displayed to other users. New items of interest may be added to a workplace. A new item added to a workplace may also be saved to the database and registered with the system for use by other users and in connection with other workplaces.

Abstract translation: 用于药物发现协作的方法和系统提供可由多个用户计算设备同时访问的协作药物发现电子工作场所。 在某些实施例中，运行服务器端应用程序的服务器计算机与多个用户计算设备通信。 服务器端应用程序与定义每个电子工作场所参数的电子数据库进行通信。 每个工作场所包括一个或多个项目的指示，例如化合物和与这些项目有关的数据，例如计算和实验数据。 一个用户对工作场所的更新可能会保存到工作场所的定义中，并传播并显示给其他用户。 可以将新的兴趣项目添加到工作场所。 添加到工作地点的新项目也可以保存到数据库中并向系统注册，供其他用户使用并与其他工作场所相关联。

公开(公告)号：WO2013163068A1

公开(公告)日：2013-10-31

申请号：PCT/US2013/037558

申请日：2013-04-22

Applicant: TARGACEPT, INC. ,  TALLAPRAGADA, Kartik ,  CHEWNING, Joseph ,  KOMBO, David ,  LUDWICK, Beverly

Inventor： TALLAPRAGADA, Kartik ,  CHEWNING, Joseph ,  KOMBO, David ,  LUDWICK, Beverly

IPC: G06F19/00 ,  G06F17/30 ,  G06F17/21

CPC classification number: G06F17/30253 ,  G06F19/707 ,  G06F19/709

Abstract: A method of obtaining chemical or molecular compound information from a document is provided. The method includes applying optical structure recognition to a document and extracting compound structure information from data obtained by applying the optical structure recognition. The method includes applying a text search module to a main body of the document and metadata of the document and extracting one or more chemical names from data obtained by applying the text search module to the main body and to the metadata. The method includes storing, in a database, an identifier, the compound structure information, and the one or more chemical names, wherein at least one method operation is executed through a processor.

Abstract translation: 提供了从文件获得化学或分子化合物信息的方法。 该方法包括对文档应用光学结构识别，并通过应用光学结构识别获得的数据提取复合结构信息。 该方法包括将文本搜索模块应用于文档的主体和文档的元数据，并从通过将文本搜索模块应用于主体和元数据而获得的数据中提取一个或多个化学名称。 该方法包括在数据库中存储标识符，复合结构信息和一个或多个化学名称，其中通过处理器执行至少一个方法操作。

公开(公告)号：WO2010060022A3

公开(公告)日：2011-05-19

申请号：PCT/US2009065490

申请日：2009-11-23

Applicant: CORNING INC ,  FANG YE ,  FERRIE ANN M ,  LAHIRI JOYDEEP ,  TRAN ELIZABETH

Inventor： FANG YE ,  FERRIE ANN M ,  LAHIRI JOYDEEP ,  TRAN ELIZABETH

IPC: G06F19/00

CPC classification number: G06F19/709 ,  G01N33/5041 ,  G01N33/54373 ,  G06F19/12

Abstract: Drug discovery is a complex undertaking facing many challenges, not the least of which is a high attrition rate as many promising candidates prove ineffective or toxic in the clinic owing to a poor understanding of the diseases, and thus the biological systems, they target. Therefore, it is broadly agreed that to increase the productivity of drug discovery one needs a far deeper understanding of the molecular mechanisms of diseases, taking into account the full biological context of the drug target and moving beyond individual genes and proteins. The present methods rely on the use of label-free cellular assays, particularly the DMR index, to systematically display the mode of actions, the toxicity, and the target(s) and pathway(s) of any molecules.

Abstract translation: 毒品发现是一项面临许多挑战的复杂工作，其中最重要的是高消耗率，因为许多有前途的候选人在诊所中证明无效或有毒，原因是对这些疾病的认识不足，从而导致其生物系统的目标。 因此，普遍同意，为了提高药物发现的生产力，需要更深入地了解疾病的分子机制，同时考虑到药物靶标的完整生物学背景，超越个别基因和蛋白质。 本方法依赖于使用无标记细胞测定法，特别是DMR指数来系统显示任何分子的作用模式，毒性以及靶标和途径。

公开(公告)号：WO2009120909A1

公开(公告)日：2009-10-01

申请号：PCT/US2009/038467

申请日：2009-03-26

Applicant: THERANOS, INC. ,  MICHELSON, Seth ,  KEMP, Timothy, Michael ,  GIBBONS, Ian ,  HOLMES, Elizabeth, A.

Inventor： MICHELSON, Seth ,  KEMP, Timothy, Michael ,  GIBBONS, Ian ,  HOLMES, Elizabeth, A.

IPC: G06F19/00 ,  G06Q50/00

CPC classification number: G06F19/3437 ,  G06F19/00 ,  G06F19/24 ,  G06F19/707 ,  G06F19/709 ,  G06Q10/00 ,  G06Q10/10 ,  G06Q50/22 ,  G16H50/50 ,  G16H50/70 ,  Y02A90/22 ,  Y02A90/26

Abstract: Described herein are methods and systems useful for characterizing clinical outcomes of a subject. Provided herein includes computer-assessed methods, medical information systems, and computer-readable instructions that can aid an end-user in diagnosis, prognosis, and treatment of a clinical outcome.

Abstract translation: 这里描述的是用于表征受试者的临床结果的方法和系统。 本文提供了计算机评估的方法，医疗信息系统和可以帮助终端用户诊断，预后和治疗临床结果的计算机可读指令。

公开(公告)号：WO2006135806A3

公开(公告)日：2008-05-02

申请号：PCT/US2006022618

申请日：2006-06-09

Applicant: CHEMIMAGE CORP ,  TREADO PATRICK J ,  SCHWEITZER ROBERT ,  NEISS JASON

Inventor： TREADO PATRICK J ,  SCHWEITZER ROBERT ,  NEISS JASON

IPC: G06F17/30 ,  G06F19/00 ,  G06F19/28

CPC classification number: G06F17/30536 ,  G06F19/703 ,  G06F19/709

Abstract: A system and method to search spectra databases and to identify unknown materials. A library having a plurality of sublibraries is provided wherein each sublibrary contains a plurality of reference data sets generated by a corresponding one of a plurality of spectroscopic data generating instruments associated with the sublibrary. Each reference data set characterizes a corresponding known material. A plurality of test data sets is provided that is characteristic of an unknown material, wherein each test data set is generated by one or more of the plurality of spectroscopic data generating instalments. For each test data set, each sublibrary is searched where the sublibrary is associated with the spectroscopic data generating instrument used to generate the test data set

Abstract translation: 搜索光谱数据库并识别未知材料的系统和方法。 提供具有多个子图库的库，其中每个子图库包含由与该子图书馆相关联的多个光谱数据生成装置中的相应一个生成的多个参考数据集。 每个参考数据集表征相应的已知材料。 提供了多个测试数据集，其是未知材料的特征，其中每个测试数据集由多个光谱数据产生分段中的一个或多个产生。 对于每个测试数据集，搜索每个子图书馆，其中子图书馆与用于生成测试数据集的光谱数据生成工具相关联

公开(公告)号：WO2007008987A1

公开(公告)日：2007-01-18

申请号：PCT/US2006/027055

申请日：2006-07-11

Applicant: eMolecules, Inc. ,  JAMES, Craig, A. ,  GUBERNATOR, Klaus

Inventor： JAMES, Craig, A. ,  GUBERNATOR, Klaus

IPC: G06F19/00

CPC classification number: G06F19/705 ,  G06F19/709

Abstract: Data that represents chemical structures, and fragments thereof, are transformed into corresponding molecular keywords comprising letters and numbers that are associated with the original data representation. These molecular keywords encode the structural features of a given chemical structure. Molecular keywords are generated for linear structures, branching points, adjacent branching points, monocyclic, polycyclic and macrocyclic ring systems, stereo centers, ring-substituent patterns and molecular-formula atom counts. Indexing, database searching, and Web page presentation can be provided in conjunction with the molecular keywords representation.

Abstract translation: 表示化学结构及其片段的数据被转换成包括与原始数据表示相关联的字母和数字的相应分子关键词。 这些分子关键词编码给定化学结构的结构特征。 对于线性结构，分支点，相邻支化点，单环，多环和大环环系统，立体中心，环取代基图案和分子原子计数生成分子关键词。 索引，数据库搜索和网页呈现可以与分子关键词表示一起提供。

公开(公告)号：WO2005022111A2

公开(公告)日：2005-03-10

申请号：PCT/IL2004/000765

申请日：2004-08-22

Applicant: YISSUM RESEARCH DEVELOPMENT COMPANY OF THE HEBREW UNIVERSITY OF JERUSALEM ,  RAYAN, Anwar ,  GOLDBLUM, Amiram

Inventor： RAYAN, Anwar ,  GOLDBLUM, Amiram

IPC: G01N

CPC classification number: G06F19/704 ,  G01N2500/00 ,  G06F19/707 ,  G06F19/709

Abstract: A stochastic algorithm has been developed for predicting the drug-likeness of molecules. It is based on optimization of ranges for a set of descriptors. Lipinski's "rule-of-5", which takes into account molecular weight, logP, and the number of hydrogen bond donor and acceptor groups for determining bioavailability, was previously unable to distinguish between drugs and non-drugs with its original set of ranges. The present invention demonstrates the predictive power of the stochastic approach to differentiate between drugs and non-drugs using only the same four descriptors of Lipinski, but modifying their ranges. However, there are better sets of 4 descriptors to differentiate between drugs and non-drugs, as many other sets of descriptors were obtained by the stochastic algorithm with more predictive power to differentiate between databases (drugs and non-drugs). A set of optimized ranges constitutes a "filter". In addition to the "best" filter, additional filters (composed of different sets of descriptors) are used that allow a new definition of "drug-like" character by combining them into a "drug like index" or DLI. In addition to producing a DLI (drug-like index), which permits discrimination between populations of drug-like and non-drug-like molecules, the present invention may be extended to be combined with other known drug screening or optimizing methods, including but not limited to, high-throughput screening, combinatorial chemistry, scaffold prioritization and docking.

Abstract translation: 已经开发了一种用于预测分子药物相似性的随机算法。 它是基于一组描述符的范围优化。 考虑到分子量，logP和用于确定生物利用度的氢键供体和受体基团的数量，Lipinski的“5号法规”以前无法区分具有其原始范围的药物和非药物。 本发明证明了利用Lipinski相同的四个描述符，但修改其范围的随机方法来区分药物和非药物的预测能力。 然而，有更好的4个描述符组合来区分药物和非药物，因为通过具有更多预测能力来区分数据库（药物和非药物）的随机算法获得了许多其他描述符集合。 一组优化的范围构成“过滤器”。 除了“最佳”过滤器之外，还使用了另外的过滤器（由不同的描述符组成），通过将它们组合成“药物样索引”或DLI，可以对“药物样”字符进行新的定义。 除了产生能够区分药物样和非药物样分子的群体之外的DLI（药物样索引）之外，本发明可以扩展到与其它已知的药物筛选或优化方法组合，包括但不限于 不限于高通量筛选，组合化学，支架优先和对接。

公开(公告)号：WO2004061728A3

公开(公告)日：2004-11-11

申请号：PCT/US0341693

申请日：2003-12-31

Applicant: MOLYSYM INC

Inventor： SHERMAN BRIAN H ,  GREEN DAVID F ,  RUPING KARL H

IPC: G06F3/00 ,  G06F3/01 ,  G06F3/033 ,  G06F19/00 ,  G06N99/00 ,  G09B23/26 ,  A63H33/04 ,  G06F17/50

CPC classification number: G06F3/0346 ,  G06F3/011 ,  G06F3/016 ,  G06F3/033 ,  G06F19/701 ,  G06F19/708 ,  G06F19/709 ,  G09B23/26

Abstract: Modeling systems are enhanced by combining physical and virtual modeling techniques to create a hybrid modeling system. Manipulation of physical models results in updated real­time physical characteristics being provided to a virtual model. User manipulation of virtual model characteristics can also be provided and implemented on the physical model using actuators and control devices. The invention also enables multiple users to simultaneously construct and manipulate different portions of a physical model, e.g., of an atom or a molecule, and to have the results of these manipulations provided to a computer system for computational analysis. The results of such analyses can be electronically returned to the physical model, e.g., wirelessly.

Abstract translation: 通过结合物理和虚拟建模技术来建立混合建模系统，建模系统得到了增强。 物理模型的操作导致提供给虚拟模型的更新的实时物理特性。 虚拟模型特征的用户操纵也可以使用致动器和控制装置在物理模型上提供和实施。 本发明还使得多个用户能够同时构建和操纵物理模型的不同部分，例如原子或分子的不同部分，并且将这些操作的结果提供给计算机系统用于计算分析。 这种分析的结果可以电子地返回到物理模型，例如无线地。