CA2427649A1 - Method for analytical jacobian computation in molecular modeling - Google Patents

Method for analytical jacobian computation in molecular modeling Download PDF

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Publication number
CA2427649A1
CA2427649A1 CA002427649A CA2427649A CA2427649A1 CA 2427649 A1 CA2427649 A1 CA 2427649A1 CA 002427649 A CA002427649 A CA 002427649A CA 2427649 A CA2427649 A CA 2427649A CA 2427649 A1 CA2427649 A1 CA 2427649A1
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CA
Canada
Prior art keywords
jacobian
equations
motion
residual
joint
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
CA002427649A
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English (en)
French (fr)
Inventor
Dan E. Rosenthal
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Protein Mechanics Inc
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Individual
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Individual filed Critical Individual
Publication of CA2427649A1 publication Critical patent/CA2427649A1/en
Abandoned legal-status Critical Current

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C10/00—Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • G16C20/62—Design of libraries

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  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Computing Systems (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Library & Information Science (AREA)
  • Medicinal Chemistry (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Complex Calculations (AREA)
  • Investigating Or Analysing Materials By Optical Means (AREA)
  • Stored Programmes (AREA)
  • Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)
  • Addition Polymer Or Copolymer, Post-Treatments, Or Chemical Modifications (AREA)
  • Magnetic Resonance Imaging Apparatus (AREA)
CA002427649A 2000-11-02 2001-11-02 Method for analytical jacobian computation in molecular modeling Abandoned CA2427649A1 (en)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US24573400P 2000-11-02 2000-11-02
US24573100P 2000-11-02 2000-11-02
US24568800P 2000-11-02 2000-11-02
US24573000P 2000-11-02 2000-11-02
US60/245,734 2000-11-02
US60/245,731 2000-11-02
US60/245,688 2000-11-02
US60/245,730 2000-11-02
PCT/US2001/051360 WO2002061662A1 (en) 2000-11-02 2001-11-02 Method for analytical jacobian computation in molecular modeling

Publications (1)

Publication Number Publication Date
CA2427649A1 true CA2427649A1 (en) 2002-08-08

Family

ID=27500199

Family Applications (3)

Application Number Title Priority Date Filing Date
CA002427649A Abandoned CA2427649A1 (en) 2000-11-02 2001-11-02 Method for analytical jacobian computation in molecular modeling
CA002427857A Abandoned CA2427857A1 (en) 2000-11-02 2001-11-02 Method for large timesteps in molecular modeling
CA002427644A Abandoned CA2427644A1 (en) 2000-11-02 2001-11-02 Method for self-validation of molecular modeling

Family Applications After (2)

Application Number Title Priority Date Filing Date
CA002427857A Abandoned CA2427857A1 (en) 2000-11-02 2001-11-02 Method for large timesteps in molecular modeling
CA002427644A Abandoned CA2427644A1 (en) 2000-11-02 2001-11-02 Method for self-validation of molecular modeling

Country Status (7)

Country Link
US (4) US20020156604A1 (https=)
EP (3) EP1344176A1 (https=)
JP (3) JP2004527027A (https=)
AU (2) AU2002234164A1 (https=)
CA (3) CA2427649A1 (https=)
IL (3) IL155685A0 (https=)
WO (4) WO2002039087A2 (https=)

Families Citing this family (36)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030187626A1 (en) * 2002-02-21 2003-10-02 Protein Mechanics, Inc. Method for providing thermal excitation to molecular dynamics models
AU2003213154A1 (en) * 2002-02-21 2003-09-09 Protein Mechanics, Inc. Method for providing thermal excitation to molecular dynamics models
AU2003262201A1 (en) * 2002-02-21 2003-10-27 Protein Mechanics, Inc. System for calculating the electrostatic force due to a system of charged bodies in molecular modeling
US20030187594A1 (en) * 2002-02-21 2003-10-02 Protein Mechanics, Inc. Method for a geometrically accurate model of solute-solvent interactions using implicit solvent
WO2003072596A2 (en) * 2002-02-27 2003-09-04 Protein Mechanics, Inc. Clustering conformational variants of molecules and methods of use thereof
CA2487454A1 (en) * 2002-05-28 2003-12-04 The Trustees Of The University Of Pennsylvania Methods, systems, and computer program products for computational analysis and design of amphiphilic polymers
US20030229476A1 (en) * 2002-06-07 2003-12-11 Lohitsa, Inc. Enhancing dynamic characteristics in an analytical model
WO2004111914A2 (en) * 2003-06-09 2004-12-23 Locus Pharmaceuticals, Inc. Efficient methods for multibody simulations
JP2006282929A (ja) * 2005-04-04 2006-10-19 Taiyo Nippon Sanso Corp 分子構造予測方法
US7752588B2 (en) * 2005-06-29 2010-07-06 Subhasis Bose Timing driven force directed placement flow
EP1907957A4 (en) * 2005-06-29 2013-03-20 Otrsotech Ltd Liability Company INVESTMENT METHODS AND SYSTEMS
JP4682791B2 (ja) * 2005-10-12 2011-05-11 ソニー株式会社 操作空間物理量算出装置及び操作空間物理量算出方法、並びにコンピュータ・プログラム
US8332793B2 (en) * 2006-05-18 2012-12-11 Otrsotech, Llc Methods and systems for placement and routing
US8739137B2 (en) 2006-10-19 2014-05-27 Purdue Research Foundation Automatic derivative method for a computer programming language
US8281299B2 (en) 2006-11-10 2012-10-02 Purdue Research Foundation Map-closure: a general purpose mechanism for nonstandard interpretation
WO2008062680A1 (en) * 2006-11-24 2008-05-29 Nec Corporation System, method and program for evaluating the performance of apparatus for predicting interaction between molecules
US7840927B1 (en) 2006-12-08 2010-11-23 Harold Wallace Dozier Mutable cells for use in integrated circuits
US7990398B2 (en) * 2007-04-13 2011-08-02 Apple Inc. Matching movement behavior in motion graphics
US7962317B1 (en) * 2007-07-16 2011-06-14 The Math Works, Inc. Analytic linearization for system design
US20090030659A1 (en) * 2007-07-23 2009-01-29 Microsoft Corporation Separable integration via higher-order programming
JP2012081568A (ja) * 2010-10-14 2012-04-26 Sony Corp ロボットの制御装置及び制御方法、並びにコンピューター・プログラム
JP5697638B2 (ja) * 2011-09-26 2015-04-08 富士フイルム株式会社 質点系の挙動を予測するシミュレーション装置およびシミュレーション方法並びにその方法を実行するためのプログラムおよび記録媒体
US9223754B2 (en) * 2012-06-29 2015-12-29 Dassault Systèmes, S.A. Co-simulation procedures using full derivatives of output variables
ES2440415B1 (es) * 2012-07-25 2015-04-13 Plebiotic, S.L. Metodo y sistema de simulacion mediante dinamica molecular con control de estabilidad
CN103034784B (zh) * 2012-12-15 2015-10-14 福州大学 基于多体系统传递矩阵的柴油机配气系统动力学计算方法
CN104076012B (zh) * 2014-07-24 2016-06-08 河南中医学院 一种近红外光谱法快速检测冰片质量的模型建立方法
US10713400B2 (en) 2017-04-23 2020-07-14 Cmlabs Simulations Inc. System and method for executing a simulation of a constrained multi-body system
CN115177123B (zh) 2018-01-17 2024-06-07 安东尼股份有限公司 安装可移动电子显示器的门
US11620418B2 (en) * 2018-03-16 2023-04-04 Autodesk, Inc. Efficient sensitivity analysis for generative parametric design of dynamic mechanical assemblies
EP3591543B1 (fr) * 2018-07-03 2023-09-06 Yf1 Système et procédé pour la simulation d'un procédé chimique ou biochimique
US10514722B1 (en) 2019-03-29 2019-12-24 Anthony, Inc. Door for mounting a removable electronic display
CN111596237B (zh) * 2020-06-01 2020-12-08 北京未磁科技有限公司 原子磁力计及其碱金属原子气室压强的原位检测方法
US20230420084A1 (en) * 2020-08-26 2023-12-28 Sanofi Scaffold Contrained Molecular Generation Using Memory Networks
CN112149328B (zh) * 2020-09-18 2022-09-30 南京理工大学 一种用于模拟分子化学趋向运动的程序算法
CN113899150B (zh) * 2021-11-08 2022-12-20 青岛海尔电冰箱有限公司 嵌入式冷冻冷藏装置及其门体连接组件
CN120012235A (zh) * 2025-01-23 2025-05-16 合肥工业大学 包含有效透射边界条件的二维结构-地基地震响应计算方法

Family Cites Families (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5025388A (en) * 1988-08-26 1991-06-18 Cramer Richard D Iii Comparative molecular field analysis (CoMFA)
US5249151A (en) * 1990-06-05 1993-09-28 Fmc Corporation Multi-body mechanical system analysis apparatus and method
US5424963A (en) * 1992-11-25 1995-06-13 Photon Research Associates, Inc. Molecular dynamics simulation method and apparatus
AU7311994A (en) * 1993-05-21 1994-12-20 Arris Pharmaceutical Corporation A machine-learning approach to modeling biological activity for molecular design and to modeling other characteristics
US5625575A (en) * 1993-08-03 1997-04-29 Lucent Technologies Inc. Apparatus for modelling interaction of rigid bodies
US5553004A (en) * 1993-11-12 1996-09-03 The Board Of Trustees Of The Leland Stanford Jr. University Constrained langevin dynamics method for simulating molecular conformations
US5745385A (en) * 1994-04-25 1998-04-28 International Business Machines Corproation Method for stochastic and deterministic timebase control in stochastic simulations
US5777889A (en) * 1994-09-22 1998-07-07 International Business Machines Corporation Method and apparatus for evaluating molecular structures using relativistic integral equations
US6341256B1 (en) * 1995-03-31 2002-01-22 Curagen Corporation Consensus configurational bias Monte Carlo method and system for pharmacophore structure determination
US5626575A (en) * 1995-04-28 1997-05-06 Conmed Corporation Power level control apparatus for electrosurgical generators
US5787279A (en) * 1995-12-22 1998-07-28 International Business Machines Corporation System and method for conformationally-flexible molecular recognition
US5752019A (en) * 1995-12-22 1998-05-12 International Business Machines Corporation System and method for confirmationally-flexible molecular identification
US6185506B1 (en) * 1996-01-26 2001-02-06 Tripos, Inc. Method for selecting an optimally diverse library of small molecules based on validated molecular structural descriptors
US5799312A (en) * 1996-11-26 1998-08-25 International Business Machines Corporation Three-dimensional affine-invariant hashing defined over any three-dimensional convex domain and producing uniformly-distributed hash keys
US6125235A (en) * 1997-06-10 2000-09-26 Photon Research Associates, Inc. Method for generating a refined structural model of a molecule
US6161080A (en) * 1997-11-17 2000-12-12 The Trustees Of Columbia University In The City Of New York Three dimensional multibody modeling of anatomical joints
US6014449A (en) * 1998-02-20 2000-01-11 Board Of Trustees Operating Michigan State University Computer-implemented system for analyzing rigidity of substructures within a macromolecule
US6253166B1 (en) * 1998-10-05 2001-06-26 The United States Of America As Represented By The Administrator Of The National Aeronautics And Space Administration Stable algorithm for estimating airdata from flush surface pressure measurements

Also Published As

Publication number Publication date
US20030018455A1 (en) 2003-01-23
IL155685A0 (en) 2003-11-23
JP2004519026A (ja) 2004-06-24
US20020156604A1 (en) 2002-10-24
AU2002239789A1 (en) 2002-05-21
WO2002057742A2 (en) 2002-07-25
JP2004534289A (ja) 2004-11-11
EP1337958A2 (en) 2003-08-27
WO2002039087A2 (en) 2002-05-16
EP1337957A2 (en) 2003-08-27
WO2002039087A3 (en) 2003-01-23
CA2427644A1 (en) 2002-07-25
WO2002036744A3 (en) 2002-07-11
WO2002036744A2 (en) 2002-05-10
JP2004527027A (ja) 2004-09-02
WO2002039087A9 (en) 2003-06-19
IL155719A0 (en) 2003-11-23
WO2002057742A3 (en) 2002-12-19
IL155686A0 (en) 2003-11-23
WO2002061662A1 (en) 2002-08-08
CA2427857A1 (en) 2002-05-16
WO2002057742A9 (en) 2003-07-17
AU2002234164A1 (en) 2002-05-15
US20030055620A1 (en) 2003-03-20
EP1344176A1 (en) 2003-09-17
US20020198695A1 (en) 2002-12-26

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