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1. WO2014138994 - SYSTEMS AND METHODS FOR IDENTIFYING THERMODYNAMIC EFFECTS OF ATOMIC CHANGES TO POLYMERS

Publication Number WO/2014/138994
Publication Date 18.09.2014
International Application No. PCT/CA2014/050240
International Filing Date 13.03.2014
IPC
G06F 19/16 2011.1
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
16for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
C12Q 1/68 2006.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
G01N 33/68 2006.1
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33Investigating or analysing materials by specific methods not covered by groups G01N1/-G01N31/131
48Biological material, e.g. blood, urine; Haemocytometers
50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
68involving proteins, peptides or amino acids
G06F 19/00 2011.1
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
CPC
G06F 17/10
GPHYSICS
06COMPUTING; CALCULATING; COUNTING
FELECTRIC DIGITAL DATA PROCESSING
17Digital computing or data processing equipment or methods, specially adapted for specific functions
10Complex mathematical operations
G06F 30/20
GPHYSICS
06COMPUTING; CALCULATING; COUNTING
FELECTRIC DIGITAL DATA PROCESSING
30Computer-aided design [CAD]
20Design optimisation, verification or simulation
G16B 15/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
15ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
Applicants
  • ZYMEWORKS INC. [CA]/[CA]
Inventors
  • LAKATOS, Gregory
  • MCWHIRTER, James Liam
Agents
  • SALISBURY, Clare
Priority Data
61/793,20315.03.2013US
61/834,75413.06.2013US
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) SYSTEMS AND METHODS FOR IDENTIFYING THERMODYNAMIC EFFECTS OF ATOMIC CHANGES TO POLYMERS
(FR) SYSTÈMES ET PROCÉDÉS PERMETTANT D'IDENTIFIER DES EFFETS THERMODYNAMIQUES DE CHANGEMENTS ATOMIQUES SUR DES POLYMÈRES
Abstract
(EN)
Systems and methods for evaluating thermodynamics of atomic changes in a polymer include using a first portion of a refined derived set of three-dimensional coordinates for a derivation of the polymer, which incorporates the atomic change under study, to compute a first effective atomistic Hessian. A second effective atomistic Hessian is computed using a second portion of a refined native set of three- dimensional coordinates for the native polymer. Atoms in the first and second portions are identical. A thermodynamic property of the first portion is determined using the refined derived set of three-dimensional coordinates and the first effective atomistic Hessian. A thermodynamic property of the second portion of the native polymer is determined using the refined native set of three-dimensional coordinates and the second effective atomistic Hessian. The effect of the atomic changes is quantified by taking the difference between the calculated thermodynamic properties of the first and second portions.
(FR)
La présente invention concerne des systèmes et des procédés permettant d'évaluer la thermodynamique de changements atomiques dans un polymère, qui consistent à utiliser une première partie d'un ensemble dérivé raffiné de coordonnées tridimensionnelles pour une dérivation du polymère, qui incorpore le changement atomique à l'étude, pour calculer une première toile de jute atomistique efficace. Une seconde toile de jute atomistique efficace est calculée à l'aide d'une seconde partie d'un ensemble natif raffiné de coordonnées tridimensionnelles pour le polymère natif. Des atomes dans les première et seconde parties sont identiques. Une propriété thermodynamique de la première partie est déterminée à l'aide de l'ensemble dérivé raffiné des coordonnées tridimensionnelles et de la première toile de jute atomistique efficace. Une propriété thermodynamique de la seconde partie du polymère natif est déterminée à l'aide de l'ensemble natif raffiné des coordonnées tridimensionnelles et de la seconde toile de jute atomistique efficace. L'effet des changements atomiques est quantifié en prenant la différence entre les propriétés thermodynamiques calculées des première et seconde parties.
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