AIMC Topic: Protein Binding

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A generative model for constructing nucleic acid sequences binding to a protein.

BMC genomics Dec 27, 2019
BACKGROUND: Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational...
Base Sequence Nucleic Acid Conformation Humans Neural Networks, Computer Algorithms Aptamers, Nucleotide Protein Binding Transcription Factors Proteins DNA
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A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information.

BMC genomics Dec 27, 2019
BACKGROUND: The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures. Many studies have suggest...
ROC Curve Protein Binding Area Under Curve Histones Neural Networks, Computer Algorithms Chromatin Histone Code
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A mitochondria-targeting nitroreductase fluorescent probe with large Stokes shift and long-wavelength emission for imaging hypoxic status in tumor cells.

Analytica chimica acta Dec 24, 2019
Development of a mitochondria-targeting fluorescent probe with large Stokes shift and long-wavelength emission was benefit for accurate detection of hypoxic status, which was known as a major factor of the tumor physiology and influence important pat...
Mitochondria Pyridinium Compounds Humans Limit of Detection Benzothiazoles Quinolinium Compounds Molecular Docking Simulation Spectrometry, Fluorescence Cell Line, Tumor Cell Hypoxia Fluorescent Dyes Protein Binding Nitroreductases Microscopy, Fluorescence
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Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks.

BMC bioinformatics Dec 24, 2019
BACKGROUND: Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past decades, detecting drug-target i...
User-Computer Interface ROC Curve Protein Binding Proteins Area Under Curve Humans Neural Networks, Computer Pharmaceutical Preparations Amino Acid Sequence Enzymes
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High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets.

Cancer immunology research Dec 23, 2019
Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response to cancer immunotherapy. Current neoantigen predictors focus on estimation of MHC binding aff...
Data Mining Mutation, Missense Histocompatibility Antigens Class II Neoplasms Neural Networks, Computer Antigens, Neoplasm Humans Protein Binding Artificial Intelligence CD8-Positive T-Lymphocytes Computational Biology Software Predictive Value of Tests Cancer Vaccines Algorithms Histocompatibility Antigens Class I
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Latest trends in structure based drug design with protein targets.

Advances in protein chemistry and structural biology Dec 18, 2019
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to d...
Molecular Docking Simulation Drug Design Antineoplastic Agents Anti-HIV Agents Protein Binding Computational Biology Neuroprotective Agents Proteins Humans Machine Learning Anti-Bacterial Agents Thermodynamics Drugs, Investigational Structure-Activity Relationship Molecular Dynamics Simulation Ligands Binding Sites
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science Dec 6, 2019
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Protein Interaction Mapping Molecular Dynamics Simulation Protein Structure, Secondary Machine Learning Ligands Protein Multimerization Software Fluorescence Resonance Energy Transfer Allosteric Site Algorithms Crystallography, X-Ray Support Vector Machine Humans Animals Protein Binding Receptors, G-Protein-Coupled Neural Networks, Computer Computational Biology Mutation
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Multimodal deep representation learning for protein interaction identification and protein family classification.

BMC bioinformatics Dec 2, 2019
BACKGROUND: Protein-protein interactions(PPIs) engage in dynamic pathological and biological procedures constantly in our life. Thus, it is crucial to comprehend the PPIs thoroughly such that we are able to illuminate the disease occurrence, achieve ...
Neural Networks, Computer Algorithms Reproducibility of Results Animals Humans Databases, Protein Area Under Curve Amino Acid Sequence Saccharomyces cerevisiae Protein Interaction Mapping Deep Learning ROC Curve Protein Binding Proteins
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MathDL: mathematical deep learning for D3R Grand Challenge 4.

Journal of computer-aided molecular design Nov 16, 2019
We present the performances of our mathematical deep learning (MathDL) models for D3R Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free energy estimation for beta secretase 1 (BACE) as well as affinity ranki...
Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Binding Sites Thermodynamics Drug Design Small Molecule Libraries Humans Deep Learning Cathepsins Molecular Docking Simulation Protein Binding Ligands
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Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.

Journal of computer-aided molecular design Nov 15, 2019
Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due to its significant role in many pathological processes, including arthritis, cancer and cardiovascular diseases. CatS inhibitors have been included in D3R-GC3 for...
Cathepsins Crystallography, X-Ray Protein Conformation Binding Sites Thermodynamics Molecular Docking Simulation Humans Protein Binding Computer-Aided Design Machine Learning Databases, Protein Ligands
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