AIMC Topic: Sequence Homology, Amino Acid

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DeepRHD: An efficient hybrid feature extraction technique for protein remote homology detection using deep learning strategies.

Computational biology and chemistry Aug 3, 2022
In computational biology, the Protein Remote homology Detection technique (PRHD) has got undeniable significance. It is mostly important for structure and function identification of a protein sequence. The previous years have seen a challenge that la...
Proteins Amino Acid Sequence Sequence Homology, Amino Acid Sequence Analysis, Protein Algorithms Deep Learning
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Identification of the tail assembly chaperone genes of T4-Like phages suggests a mechanism other than translational frameshifting for biogenesis of their encoded proteins.

Virology Nov 18, 2021
Tape measure (TM) proteins are essential for the formation of long-tailed phages. TM protein assembly into tails requires the action of tail assembly chaperones (TACs). TACs (e.g. gpG and gpT of E. coli phage lambda) are usually produced in a short (...
Bacteriophage T4 Amino Acid Sequence Bacteria Molecular Chaperones Conserved Sequence Genome, Viral Frameshifting, Ribosomal Computational Biology Viral Tail Proteins Sequence Alignment Escherichia coli Virion Sequence Homology, Amino Acid Virus Assembly
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ECNet is an evolutionary context-integrated deep learning framework for protein engineering.

Nature communications Sep 30, 2021
Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited....
High-Throughput Screening Assays Datasets as Topic Protein Engineering Sequence Homology, Amino Acid Mutation Amino Acid Sequence beta-Lactamases Deep Learning beta-Lactam Resistance Evolution, Molecular Genetic Fitness
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Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.

PLoS computational biology Mar 22, 2021
Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally ch...
Protein Conformation Cations Evolution, Molecular Substrate Specificity Plants Machine Learning Sequence Homology, Amino Acid Amino Acid Sequence Alkyl and Aryl Transferases Sesquiterpenes
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Computational approach for identification, characterization, three-dimensional structure modelling and machine learning-based thermostability prediction of xylanases from the genome of Aspergillus fumigatus.

Computational biology and chemistry Feb 6, 2021
Identification of thermostable and alkaline xylanases from different fungal and bacterial species have gained an interest for the researchers because of its biotechnological relevance in many industries, such as pulp, paper, and bioethanol. In this s...
Machine Learning Temperature Aspergillus fumigatus Enzyme Stability Protein Conformation Endo-1,4-beta Xylanases Molecular Docking Simulation Computational Biology Amino Acid Sequence Data Mining Sequence Homology, Amino Acid Genome, Fungal
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DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures.

Proteins Sep 16, 2020
Accurate prediction of protein secondary structure (alpha-helix, beta-strand and coil) is a crucial step for protein inter-residue contact prediction and ab initio tertiary structure prediction. In a previous study, we developed a deep belief network...
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Markov Chains Sequence Alignment Sequence Homology, Amino Acid Neural Networks, Computer Software Deep Learning Proteins Databases, Protein Amino Acid Sequence
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Machine-learning approach expands the repertoire of anti-CRISPR protein families.

Nature communications Jul 29, 2020
The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechani...
Host-Parasite Interactions Viral Proteins Sequence Homology, Amino Acid Sequence Analysis, Protein Gene Editing CRISPR-Associated Protein 9 Machine Learning Archaea Bacteria Bacteriophages Computational Biology CRISPR-Cas Systems Datasets as Topic
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De novo profile generation based on sequence context specificity with the long short-term memory network.

BMC bioinformatics Jul 18, 2018
BACKGROUND: Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Ami...
Amino Acid Sequence Databases as Topic Sequence Homology, Amino Acid Deep Learning ROC Curve Neural Networks, Computer Computational Biology Proteins
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Thermodynamics Sequence Alignment Sequence Homology, Amino Acid Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Animals Protein Conformation, beta-Strand Protein Binding Point Mutation Models, Molecular Serotonin 5-HT2 Receptor Agonists Receptor, Serotonin, 5-HT2C Humans Kinetics Gene Expression Serotonin 5-HT2 Receptor Antagonists Crystallography, X-Ray Machine Learning Amino Acid Sequence Binding Sites Protein Stability Protein Engineering
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Functional Annotation of Proteins Encoded by the Minimal Bacterial Genome Based on Secondary Structure Element Alignment.

Journal of proteome research May 24, 2018
In synthetic biology, one of the key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0,...
Supervised Machine Learning Molecular Sequence Annotation Genome, Bacterial Protein Structure, Secondary Artificial Intelligence Sequence Homology, Amino Acid Algorithms Bacterial Proteins
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