AIMC Topic: Enzymes

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ABLE: Attention based learning for enzyme classification.

Computational biology and chemistry Aug 19, 2021
Classifying proteins into their respective enzyme class is an interesting question for researchers for a variety of reasons. The open source Protein Data Bank (PDB) contains more than 1,60,000 structures, with more being added everyday. This paper pr...
Neural Networks, Computer Machine Learning Enzymes
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A hierarchical deep learning based approach for multi-functional enzyme classification.

Protein science : a publication of the Protein Society Jun 28, 2021
Enzymes are critical proteins in every organism. They speed up essential chemical reactions, help fight diseases, and have a wide use in the pharmaceutical and manufacturing industries. Wet lab experiments to figure out an enzyme's function are time ...
Deep Learning Structure-Activity Relationship Datasets as Topic Terminology as Topic Enzymes Biocatalysis
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Machine learning differentiates enzymatic and non-enzymatic metals in proteins.

Nature communications Jun 17, 2021
Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is challenging to differentiate b...
Metals Databases, Protein Models, Molecular Machine Learning Algorithms Binding Sites Enzymes Metalloproteins Catalytic Domain Static Electricity Catalysis
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The rise of intelligent matter.

Nature Jun 16, 2021
Artificial intelligence (AI) is accelerating the development of unconventional computing paradigms inspired by the abilities and energy efficiency of the brain. The human brain excels especially in computationally intensive cognitive tasks, such as p...
Physical Stimulation Skin, Artificial Biomimetic Materials Homeostasis Environment Robotics Enzymes Equipment Design Humans Biomimetics Colloids Artificial Intelligence
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Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification.

Bioinformatics (Oxford, England) Jan 30, 2021
MOTIVATION: As experimental efforts are costly and time consuming, computational characterization of enzyme capabilities is an attractive alternative. We present and evaluate several machine-learning models to predict which of 983 distinct enzymes, a...
Computational Biology Databases, Protein Substrate Specificity Enzymes Enzyme Inhibitors Neural Networks, Computer Machine Learning
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BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint.

BMC bioinformatics Jul 23, 2020
BACKGROUND: Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such represen...
Databases, Factual Enzymes Knowledge Bases Metabolism Biological Ontologies
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A Machine Learning Approach for Drug-target Interaction Prediction using Wrapper Feature Selection and Class Balancing.

Molecular informatics Feb 11, 2020
Drug-Target interaction (DTI) plays a crucial role in drug discovery, drug repositioning and understanding the drug side effects which helps to identify new therapeutic profiles for various diseases. However, the exponential growth in the genomic and...
Machine Learning Receptors, Cytoplasmic and Nuclear Receptors, G-Protein-Coupled Computer Simulation Enzymes Pharmaceutical Preparations Algorithms Drug Development Drug Discovery Databases, Chemical Amino Acid Sequence Databases, Protein Ion Channels
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Reinforcement Learning for Bioretrosynthesis.

ACS synthetic biology Dec 30, 2019
Metabolic engineering aims to produce chemicals of interest from living organisms, to advance toward greener chemistry. Despite efforts, the research and development process is still long and costly, and efficient computational design tools are requi...
Metabolic Engineering Algorithms Metabolic Networks and Pathways Models, Biological Artificial Intelligence Software Markov Chains Reinforcement, Psychology Monte Carlo Method Synthetic Biology Enzymes
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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...
Proteins User-Computer Interface Pharmaceutical Preparations Area Under Curve Amino Acid Sequence ROC Curve Humans Enzymes Protein Binding Neural Networks, Computer
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Identifying pseudoenzymes using functional annotation: pitfalls of common practice.

The FEBS journal Dec 5, 2019
Pseudoenzymes are proteins that are evolutionary related to enzymes but lack relevant catalytic activity. They are usually evolved from enzymatic ancestors that have lost their catalytic activities. The loss of catalytic function is one extreme among...
Enzymes Proteins Knowledge Bases Molecular Sequence Annotation Humans
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