Hudson et al., 2018 - Google Patents
Force matching as a stepping stone to QM/MM CB [8] host/guest binding free energies: a SAMPL6 cautionary taleHudson et al., 2018
View HTML- Document ID
- 3198604788510173759
- Author
- Hudson P
- Han K
- Woodcock H
- Brooks B
- Publication year
- Publication venue
- Journal of computer-aided molecular design
External Links
Snippet
Use of quantum mechanical/molecular mechanical (QM/MM) methods in binding free energy calculations, particularly in the SAMPL challenge, often fail to achieve improvement over standard additive (MM) force fields. Frequently, the implementation is through use of …
- 230000027455 binding 0 title abstract description 27
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
- G06F19/70—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
-
- 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
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by the preceding groups
- G01N33/48—Investigating or analysing materials by specific methods not covered by the preceding groups biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
-
- 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
- G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
-
- 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
- G06F19/704—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for prediction of properties of compounds, e.g. calculating and selecting molecular descriptors, details related to the development of SAR/QSAR/QSPR models, ADME/Tox models or PK/PD models
-
- 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
- G06F19/708—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for data visualisation, e.g. molecular structure representations, graphics generation, display of maps or networks or other visual representations
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
-
- 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
-
- 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
- G06F19/707—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds using machine learning, data mining or chemometrics, e.g. pattern recognition, knowledge discovery, rule extraction, correlation, clustering or classification, chemical name to structure conversion
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F11/00—Error detection; Error correction; Monitoring
- G06F11/07—Error detection; Error correction; Monitoring responding to the occurence of a fault, e.g. fault tolerance
- G06F11/16—Error detection or correction of the data by redundancy in hardware
- G06F11/1658—Data re-synchronization of a redundant component, or initial sync of replacement, additional or spare unit
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Hudson et al. | Force matching as a stepping stone to QM/MM CB [8] host/guest binding free energies: a SAMPL6 cautionary tale | |
Cole et al. | Biomolecular force field parameterization via atoms-in-molecule electron density partitioning | |
Heinzelmann et al. | Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation | |
Gapsys et al. | Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches | |
Liu et al. | Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations | |
Daily et al. | Allosteric communication occurs via networks of tertiary and quaternary motions in proteins | |
CN1886659B (en) | Method and system for computing inter-molecule subsets affinity function of molecular configuration | |
Bernetti et al. | An integrated Markov state model and path metadynamics approach to characterize drug binding processes | |
Mikulskis et al. | Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies | |
Gu et al. | Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis | |
Yin et al. | The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method | |
Rogers et al. | Probing the thermodynamics of competitive ion binding using minimum energy structures | |
Aldeghi et al. | Absolute alchemical free energy calculations for ligand binding: A beginner’s guide | |
Hu et al. | The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP | |
Genheden et al. | Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge | |
Zhang et al. | Evaluation of generalized born models for large scale affinity prediction of cyclodextrin host–guest complexes | |
Khalak et al. | Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software | |
Pickard et al. | Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p K a corrections | |
König et al. | Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge | |
Sun | SAMPL7 trimertrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations | |
Réblová et al. | A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis | |
Eken et al. | SAMPL6 host–guest challenge: binding free energies via a multistep approach | |
Han et al. | Prediction of CB [8] host–guest binding free energies in SAMPL6 using the double-decoupling method | |
Li et al. | Exploring the effect of D61G mutation on SHP2 cause gain of function activity by a molecular dynamics study | |
Nishikawa et al. | Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges |