AIMC Topic: Proteins

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Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions.

Journal of computer-aided molecular design Nov 14, 2019
The computational prediction of ligand-biopolymer affinities is a crucial endeavor in modern drug discovery and one that still poses major challenges. The choice of the appropriate computational method often reveals itself as a trade-off between accu...
Protein Binding Proteins Databases, Protein Ligands Machine Learning Algorithms Drug Discovery Humans
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ALADDIN: Docking Approach Augmented by Machine Learning for Protein Structure Selection Yields Superior Virtual Screening Performance.

Molecular informatics Nov 8, 2019
Protein flexibility and solvation pose major challenges to docking algorithms and scoring functions. One established strategy for addressing these challenges is to use multiple protein conformations for docking (all-against-all ensemble docking). Rec...
Molecular Docking Simulation Proteins Protein Conformation Machine Learning Algorithms
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Characterization and Identification of Lysine Succinylation Sites based on Deep Learning Method.

Scientific reports Nov 7, 2019
Succinylation is a type of protein post-translational modification (PTM), which can play important roles in a variety of cellular processes. Due to an increasing number of site-specific succinylated peptides obtained from high-throughput mass spectro...
Succinic Acid Sequence Analysis, Protein Proteins Databases, Protein Lysine Deep Learning Protein Processing, Post-Translational
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Inexpensive robotic system for standard and fluorescent imaging of protein crystals.

Acta crystallographica. Section F, Structural biology communications Nov 5, 2019
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over $100 000. This cost puts the use of crystallization-trial imaging outside the reach o...
Printing, Three-Dimensional Proteins Robotics Animals Chickens Costs and Cost Analysis Optical Imaging Muramidase Fluorescent Dyes Lasers Crystallization Software
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Constructive Prediction of Potential RNA Aptamers for a Protein Target.

IEEE/ACM transactions on computational biology and bioinformatics Nov 4, 2019
Aptamers are short single-stranded nucleic acids that bind to target molecules with high affinity and selectivity. Aptamers are generally identified in vitro by performing SELEX (systematic evolution of ligands by exponential enrichment). Complementi...
Proteins RNA Protein Structure, Secondary Support Vector Machine Decision Trees Aptamers, Nucleotide SELEX Aptamer Technique Protein Binding Computational Biology
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Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions.

Journal of chemical information and modeling Oct 31, 2019
Structure-based drug design is critically dependent on accuracy of molecular docking scoring functions, and there is of significant interest to advance scoring functions with machine learning approaches. In this work, by judiciously expanding the tra...
Ligands Molecular Conformation Small Molecule Libraries Protein Binding Proteins Databases, Protein Drug Design Water Humans Machine Learning Molecular Docking Simulation
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Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.

BMC bioinformatics Oct 29, 2019
BACKGROUND: Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective in inferring inter-residue contacts. The Markov ran...
Algorithms Proteins Deep Learning Probability
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Recognizing five molecular ligand-binding sites with similar chemical structure.

Journal of computational chemistry Oct 23, 2019
Accurate identification of ligand-binding sites and discovering the protein-ligand interaction mechanism are important for understanding proteins' functions and designing new drugs. Meanwhile, accurate computational prediction and mechanism research ...
Ligands Binding Sites NAD Proteins Adenosine Triphosphate Guanosine Triphosphate Adenosine Diphosphate Guanosine Diphosphate Support Vector Machine
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Improving neural protein-protein interaction extraction with knowledge selection.

Computational biology and chemistry Oct 23, 2019
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein entities and thei...
Knowledge Bases Proteins Datasets as Topic Models, Molecular Protein Interaction Mapping
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Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.

Journal of computer-aided molecular design Oct 18, 2019
In the current "genomic era" the number of identified genes is growing exponentially. However, the biological function of a large number of the corresponding proteins is still unknown. Recognition of small molecule ligands (e.g., substrates, inhibito...
Humans Sequence Homology Artificial Intelligence Proteins Drug Design Machine Learning Models, Molecular Ligands Protein Binding Software Amino Acid Sequence Protein Conformation Computational Biology Small Molecule Libraries
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