AIMC Topic: Amino Acid Sequence

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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...
Pharmaceutical Preparations Amino Acid Sequence Enzymes Protein Binding Proteins Area Under Curve User-Computer Interface ROC Curve Humans Neural Networks, Computer
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iQSP: A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou's 5-Steps Rule and Informative Physicochemical Properties.

International journal of molecular sciences Dec 20, 2019
Understanding of quorum-sensing peptides (QSPs) in their functional mechanism plays an essential role in finding new opportunities to combat bacterial infections by designing drugs. With the avalanche of the newly available peptide sequences in the p...
Amino Acid Sequence Bacterial Physiological Phenomena Quorum Sensing Bacteria Support Vector Machine Models, Molecular Machine Learning Peptides Drug Discovery
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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...
Proteomics Proteins Databases, Protein Neural Networks, Computer Machine Learning Computational Biology Databases, Nucleic Acid Sequence Analysis Natural Language Processing 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 Software Amino Acid Sequence Knowledge Bases
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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 ...
Deep Learning Humans Algorithms ROC Curve Amino Acid Sequence Protein Binding Proteins Neural Networks, Computer Reproducibility of Results Saccharomyces cerevisiae Databases, Protein Protein Interaction Mapping Animals Area Under Curve
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Sounds interesting: can sonification help us design new proteins?

Expert review of proteomics Nov 27, 2019
: The practice of turning scientific data into music, a practice known as sonification, is a growing field. Driven by analogies between the hierarchical structures of proteins and many forms of music, multiple attempts of mapping proteins to music ha...
Protein Engineering Protein Structure, Secondary Music Machine Learning Proteins Humans Amino Acid Sequence
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Introducing of an integrated artificial neural network and Chou's pseudo amino acid composition approach for computational epitope-mapping of Crimean-Congo haemorrhagic fever virus antigens.

International immunopharmacology Nov 24, 2019
This study was aimed to introduce a novel algorithm for determining linear B- and T-cell epitopes from Crimean-Congo haemorrhagic fever virus (CCHFV) antigens. To this end, 387 approved B- and T-cell epitopes, as well as 331 non-epitope peptides from...
Amino Acid Sequence Hemorrhagic Fever, Crimean Humans Datasets as Topic Neural Networks, Computer Epitopes, B-Lymphocyte Antigens, Viral Peptide Library Viral Proteins Epitope Mapping Epitopes, T-Lymphocyte Computational Biology Protein Structure, Tertiary Hemorrhagic Fever Virus, Crimean-Congo Support Vector Machine Molecular Docking Simulation Histocompatibility Antigens Class II
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AGONOTES: A Robot Annotator for Argonaute Proteins.

Interdisciplinary sciences, computational life sciences Nov 18, 2019
The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered fo...
Algorithms Computational Biology Robotics Amino Acid Sequence Prokaryotic Cells Argonaute Proteins
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An improved deep learning method for predicting DNA-binding proteins based on contextual features in amino acid sequences.

PloS one Nov 14, 2019
As the number of known proteins has expanded, how to accurately identify DNA binding proteins has become a significant biological challenge. At present, various computational methods have been proposed to recognize DNA-binding proteins from only amin...
Reproducibility of Results Amino Acid Sequence Neural Networks, Computer Memory, Long-Term Deep Learning Algorithms DNA-Binding Proteins
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SDBP-Pred: Prediction of single-stranded and double-stranded DNA-binding proteins by extending consensus sequence and K-segmentation strategies into PSSM.

Analytical biochemistry Nov 3, 2019
Identification of DNA-binding proteins (DNA-BPs) is a hot issue in protein science due to its key role in various biological processes. These processes are highly concerned with DNA-binding protein types. DNA-BPs are classified into single-stranded D...
DNA-Binding Proteins Computational Biology Amino Acid Sequence Support Vector Machine Datasets as Topic Consensus Sequence Databases, Protein
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