AIMC Topic: Proteins

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Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter.

BMC genomics Dec 27, 2019
BACKGROUND: Identification of protein-protein interactions (PPIs) is crucial for understanding biological processes and investigating the cellular functions of genes. Self-interacting proteins (SIPs) are those in which more than two identical protein...
Support Vector Machine Proteins Principal Component Analysis Area Under Curve Saccharomyces cerevisiae Databases, Protein Humans Saccharomyces cerevisiae Proteins ROC Curve Protein Interaction Maps
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Machine learning for protein folding and dynamics.

Current opinion in structural biology Dec 24, 2019
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools. The way si...
Protein Folding Machine Learning Proteins Models, Molecular
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MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.

BMC genomics Dec 24, 2019
BACKGROUND: Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database sea...
HeLa Cells Proteins Tandem Mass Spectrometry Sequence Analysis, Protein Humans Neural Networks, Computer Peptides Deep Learning
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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...
Amino Acid Sequence Enzymes Area Under Curve Pharmaceutical Preparations Neural Networks, Computer User-Computer Interface Protein Binding Proteins ROC Curve Humans
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Molecular Insights from Conformational Ensembles via Machine Learning.

Biophysical journal Dec 21, 2019
Biomolecular simulations are intrinsically high dimensional and generate noisy data sets of ever-increasing size. Extracting important features from the data is crucial for understanding the biophysical properties of molecular processes, but remains ...
Proteins Protein Conformation Humans Machine Learning
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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...
Structure-Activity Relationship Drugs, Investigational Drug Design Molecular Dynamics Simulation Binding Sites Neuroprotective Agents Anti-Bacterial Agents Antineoplastic Agents Ligands Thermodynamics Proteins Humans Molecular Docking Simulation Protein Binding Anti-HIV Agents Machine Learning Computational Biology
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Modeling aspects of the language of life through transfer-learning protein sequences.

BMC bioinformatics Dec 17, 2019
BACKGROUND: Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary information. However, for some applica...
Neural Networks, Computer Proteomics Proteins Databases, Protein Machine Learning Computational Biology Databases, Nucleic Acid Natural Language Processing Sequence Analysis Amino Acid Sequence
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UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase).

Journal of proteomics Dec 14, 2019
UniprotR is a software package designed to easily retrieve, cluster and visualize protein data from UniProt knowledgebase (UniProtKB) using R language. The package is implemented mainly to process, parse and illustrate proteomics data in a handy and ...
Phylogeny Proteins Knowledge Bases Software Amino Acid Sequence
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Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.

Nature methods Dec 9, 2019
Predicting interactions between proteins and other biomolecules solely based on structure remains a challenge in biology. A high-level representation of protein structure, the molecular surface, displays patterns of chemical and geometric features th...
Proteins Surface Properties Protein Conformation Deep Learning Computational Biology Algorithms
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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...
Knowledge Bases Molecular Sequence Annotation Enzymes Humans Proteins
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