[go: up one dir, main page]
More Web Proxy on the site http://driver.im/

Tran-Nguyen et al., 2020 - Google Patents

LIT-PCBA: an unbiased data set for machine learning and virtual screening

Tran-Nguyen et al., 2020

View PDF
Document ID
12689080403348380538
Author
Tran-Nguyen V
Jacquemard C
Rognan D
Publication year
Publication venue
Journal of chemical information and modeling

External Links

Snippet

Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ligand …
Continue reading at hal.science (PDF) (other versions)

Classifications

    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/16Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/706Chemoinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/18Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/24Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/20Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/12Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/30Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
    • G06F19/34Computer-assisted medical diagnosis or treatment, e.g. computerised prescription or delivery of medication or diets, computerised local control of medical devices, medical expert systems or telemedicine
    • G06F19/345Medical expert systems, neural networks or other automated diagnosis
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/708Chemoinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/704Chemoinformatics, 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
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by the preceding groups
    • G01N33/48Investigating or analysing materials by specific methods not covered by the preceding groups biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803General methods of protein analysis not limited to specific proteins or families of proteins
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by the preceding groups
    • G01N33/48Investigating or analysing materials by specific methods not covered by the preceding groups biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F11/00Error detection; Error correction; Monitoring
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F3/00Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06NCOMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N99/00Subject matter not provided for in other groups of this subclass
    • G06N99/005Learning machines, i.e. computer in which a programme is changed according to experience gained by the machine itself during a complete run

Similar Documents

Publication Publication Date Title
Tran-Nguyen et al. LIT-PCBA: an unbiased data set for machine learning and virtual screening
Francoeur et al. Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design
Yang et al. Efficient exploration of chemical space with docking and deep learning
Dhakal et al. Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions
Volkov et al. On the frustration to predict binding affinities from protein–ligand structures with deep neural networks
Lim et al. Predicting drug–target interaction using a novel graph neural network with 3D structure-embedded graph representation
Ashtawy et al. Task-specific scoring functions for predicting ligand binding poses and affinity and for screening enrichment
Cross et al. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy
Jiménez et al. K deep: protein–ligand absolute binding affinity prediction via 3d-convolutional neural networks
Desaphy et al. Comparison and druggability prediction of protein–ligand binding sites from pharmacophore-annotated cavity shapes
Gabel et al. Beware of Machine Learning-Based Scoring Functions On the Danger of Developing Black Boxes
Wagner et al. POVME 3.0: software for mapping binding pocket flexibility
Hawkins Conformation generation: the state of the art
Tian et al. Assessing an ensemble docking-based virtual screening strategy for kinase targets by considering protein flexibility
Hu et al. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening
Friedrich et al. High-quality dataset of protein-bound ligand conformations and its application to benchmarking conformer ensemble generators
Li et al. Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results
Scantlebury et al. Data set augmentation allows deep learning-based virtual screening to better generalize to unseen target classes and highlight important binding interactions
Venkatraman et al. Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods
Singh et al. AADS-An automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors
Berenger et al. Lean-docking: exploiting ligands’ predicted docking scores to accelerate molecular docking
Schomburg et al. Facing the challenges of structure-based target prediction by inverse virtual screening
Lagarde et al. Benchmarking data sets for the evaluation of virtual ligand screening methods: review and perspectives
Tran-Nguyen et al. True accuracy of fast scoring functions to predict high-throughput screening data from docking poses: the simpler the better
Ricci-Lopez et al. Improving structure-based virtual screening with ensemble docking and machine learning