[go: up one dir, main page]

Ranaghan et al., 2010 - Google Patents

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods

Ranaghan et al., 2010

Document ID
11678999284534760785
Author
Ranaghan K
Mulholland A
Publication year
Publication venue
International Reviews in Physical Chemistry

External Links

Snippet

Combined quantum mechanics/molecular mechanics (QM/MM or QM-MM) methods are an excellent approach for modelling the mechanisms of enzyme-catalysed reactions. QM/MM methods allow detailed modelling of reactions in enzymes by coupling quantum chemical …
Continue reading at www.tandfonline.com (other versions)

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/16—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for 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
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/12—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for modelling or simulation in systems biology, e.g. probabilistic or dynamic models, gene-regulatory networks, protein interaction networks or metabolic networks
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICRO-ORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING OR MAINTAINING MICRO-ORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/706—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for drug design with the emphasis on a therapeutic agent, e.g. ligand-biological target interactions, pharmacophore generation

Similar Documents

Publication Publication Date Title
Ranaghan et al. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods
Van Der Kamp et al. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology
Romero-Rivera et al. Computational tools for the evaluation of laboratory-engineered biocatalysts
Romero-Rivera et al. Role of conformational dynamics in the evolution of retro-aldolase activity
Nichols et al. Ligand-induced proton transfer and low-barrier hydrogen bond revealed by X-ray crystallography
Kiss et al. Computational enzyme design
Lonsdale et al. Computational enzymology
Sirin et al. A computational approach to enzyme design: Predicting ω-aminotransferase catalytic activity using docking and MM-GBSA scoring
Gao et al. Mechanisms and free energies of enzymatic reactions
Sirin et al. Physics‐based enzyme design: Predicting binding affinity and catalytic activity
Quartararo et al. Structural, kinetic and chemical mechanism of isocitrate dehydrogenase-1 from Mycobacterium tuberculosis
Novelli et al. Quantitative measurement of intrinsic GTP hydrolysis for carcinogenic glutamine 61 mutants in H-Ras
Veeraraghavan et al. Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation
Glaser et al. Hit expansion of a noncovalent SARS-CoV-2 main protease inhibitor
Rinaldi et al. Understanding complex mechanisms of enzyme reactivity: the case of Limonene-1, 2-epoxide hydrolases
Zhu et al. Ring contraction catalyzed by the metal-dependent radical SAM enzyme: 7-carboxy-7-deazaguanine synthase from B. multivorans. Theoretical insights into the reaction mechanism and the influence of metal ions
Douglas-Gallardo et al. Carbon dioxide fixation in RuBisCO is protonation-state-dependent and irreversible
Medina et al. Water molecules allow the intramolecular activation of the thiamine di-phosphate cofactor in human transketolase: Mechanistic insights into a famous proposal
Hix et al. Combining evolutionary conservation and quantum topological analyses to determine quantum mechanics subsystems for biomolecular quantum mechanics/molecular mechanics simulations
Korbeld et al. Curse and blessing of non‐proteinogenic parts in computational enzyme engineering
Ahsan et al. Water plays a cocatalytic role in epoxide ring opening reaction in aspartate proteases: a QM/MM study
Kędzierski et al. Catalytic Fields as a Tool to Analyze Enzyme Reaction Mechanism Variants and Reaction Steps
Schramm et al. Backbone flexibility, conformational change, and catalysis in a phosphohexomutase from Pseudomonas aeruginosa
Xiong et al. Potency prediction of covalent inhibitors against SARS-CoV-2 3CL-like protease and multiple mutants by multiscale simulations
Bitra et al. Identification of function and mechanistic insights of guanine deaminase from Nitrosomonas europaea: role of the C-terminal loop in catalysis