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

Davila et al., 2022 - Google Patents

AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence

Davila et al., 2022

View HTML @Full View
Document ID
6164944094053738125
Author
Davila A
Xu Z
Li S
Rozewicki J
Wilamowski J
Kotelnikov S
Kozakov D
Teraguchi S
Standley D
Publication year
Publication venue
Bioinformatics Advances

External Links

Snippet

Motivation The scoring of antibody–antigen docked poses starting from unbound homology models has not been systematically optimized for a large and diverse set of input sequences. Results To address this need, we have developed AbAdapt, a webserver that …
Continue reading at academic.oup.com (HTML) (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
    • G06F19/28Bioinformatics, 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
    • G06F19/10Bioinformatics, 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
    • G06F19/22Bioinformatics, 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
    • G06F19/18Bioinformatics, 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
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30386Retrieval requests
    • 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
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30861Retrieval from the Internet, e.g. browsers
    • G06F17/30864Retrieval from the Internet, e.g. browsers by querying, e.g. search engines or meta-search engines, crawling techniques, push systems
    • G06F17/30867Retrieval from the Internet, e.g. browsers by querying, e.g. search engines or meta-search engines, crawling techniques, push systems with filtering and personalisation
    • 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
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/3061Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
    • 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
    • G06F19/32Medical data management, e.g. systems or protocols for archival or communication of medical images, computerised patient records or computerised general medical references
    • 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
    • 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
    • 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06QDATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
    • G06Q50/00Systems or methods specially adapted for a specific business sector, e.g. utilities or tourism
    • G06Q50/10Services
    • G06Q50/22Health care, e.g. hospitals; Social work

Similar Documents

Publication Publication Date Title
Stein et al. SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2
Northey et al. IntPred: a structure-based predictor of protein–protein interaction sites
Nussinov et al. AlphaFold, artificial intelligence (AI), and allostery
Davila et al. AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence
Wang et al. Enhanced prediction of hot spots at protein-protein interfaces using extreme gradient boosting
Krapp et al. PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces
Brenke et al. Application of asymmetric statistical potentials to antibody–protein docking
Bliven et al. Automated evaluation of quaternary structures from protein crystals
Disfani et al. MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
Qi et al. Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
Lyskov et al. The RosettaDock server for local protein–protein docking
de Vries et al. CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK
Saladin et al. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces
Jain et al. Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning
Abdin et al. PepNN: a deep attention model for the identification of peptide binding sites
Chen et al. Systematic evaluation of machine learning methods for identifying human–pathogen protein–protein interactions
Li et al. Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms
Peng et al. EnANNDeep: an ensemble-based lncRNA–protein interaction prediction framework with adaptive k-nearest neighbor classifier and deep models
Makigaki et al. Sequence alignment using machine learning for accurate template-based protein structure prediction
Hou et al. SeRenDIP-CE: sequence-based interface prediction for conformational epitopes
Won et al. 3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints
Liu et al. HPOLabeler: improving prediction of human protein–phenotype associations by learning to rank
Li et al. PredAmyl‐MLP: Prediction of Amyloid Proteins Using Multilayer Perceptron
Li et al. Large-scale identification of human protein function using topological features of interaction network
Simm et al. Critical assessment of coiled-coil predictions based on protein structure data