AIMC Topic: Sequence Homology, Amino Acid

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MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Journal of molecular biology Mar 10, 2018
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO,...
Protein Interaction Mapping Sequence Homology, Amino Acid Sequence Analysis, Protein Internet Amino Acid Sequence Protein Conformation Gene Ontology Protein Interaction Maps Computational Biology Proteins Models, Molecular Software Algorithms Reproducibility of Results
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ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods.

IEEE/ACM transactions on computational biology and bioinformatics Jan 5, 2018
As one of the most challenging tasks in sequence analysis, protein remote homology detection has been extensively studied. Methods based on discriminative models and ranking approaches have achieved the state-of-the-art performance, and these two kin...
Proteins Databases, Protein Sequence Homology, Amino Acid Amino Acid Motifs Sequence Analysis, Protein Databases, Factual Reproducibility of Results Humans Computational Biology Neural Networks, Computer Support Vector Machine Software Algorithms
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Extracting features from protein sequences to improve deep extreme learning machine for protein fold recognition.

Journal of theoretical biology Mar 27, 2017
Protein fold recognition is an important problem in bioinformatics to predict three-dimensional structure of a protein. One of the most challenging tasks in protein fold recognition problem is the extraction of efficient features from the amino-acid ...
Computational Biology Principal Component Analysis Amino Acid Sequence Datasets as Topic Protein Conformation Protein Folding Sequence Homology, Amino Acid Sequence Analysis, Protein Machine Learning
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WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

PLoS computational biology Nov 3, 2016
The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital componen...
Pattern Recognition, Automated Sequence Homology, Amino Acid Genetic Speciation Evolution, Molecular Proteins Genetic Variation High-Throughput Nucleotide Sequencing Machine Learning Software Algorithms Animals Humans
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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

Immunogenetics Sep 29, 2015
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented ...
Peptide Fragments Epitopes Amino Acid Sequence Binding Sites Computational Biology Humans Algorithms Cluster Analysis Neural Networks, Computer Animals Molecular Sequence Data Databases, Protein Protein Binding Sequence Homology, Amino Acid Models, Molecular Mice Histocompatibility Antigens Class II
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Knockdown of NADPH-cytochrome P450 reductase results in reduced resistance to buprofezin in the small brown planthopper, Laodelphax striatellus (fallén).

Pesticide biochemistry and physiology Sep 5, 2015
NADPH-cytochrome P450 reductase (CPR) plays an important role in cytochrome P450 function, and CPR knockdown in several insects leads to increased susceptibility to insecticides. However, a putative CPR gene has not yet been fully characterized in th...
Sequence Homology, Amino Acid Hemiptera Animals Thiadiazines Phylogeny Molecular Sequence Data Amino Acid Sequence Insecticide Resistance Cloning, Molecular NADPH-Ferrihemoprotein Reductase
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.

Proceedings of the National Academy of Sciences of the United States of America Apr 13, 2021
In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth ...
Unsupervised Machine Learning Amino Acids Protein Conformation Sequence Homology, Amino Acid Sequence Analysis, Protein
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The PSIPRED Protein Analysis Workbench: 20 years on.

Nucleic acids research Jul 2, 2019
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 year...
Models, Molecular Internet Amino Acid Sequence History, 21st Century Software Protein Binding Proteins Molecular Sequence Annotation Sequence Homology, Amino Acid Gene Ontology Protein Interaction Domains and Motifs Binding Sites Protein Conformation, alpha-Helical Sequence Alignment Protein Conformation, beta-Strand
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NetGO: improving large-scale protein function prediction with massive network information.

Nucleic acids research Jul 2, 2019
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...
Amino Acid Sequence Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Humans Models, Molecular Machine Learning Internet Computational Biology Software Benchmarking Proteins Animals Plants Databases, Protein Structure-Activity Relationship Sequence Alignment Sequence Homology, Amino Acid Sequence Analysis, Protein Prokaryotic Cells
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ComplexContact: a web server for inter-protein contact prediction using deep learning.

Nucleic acids research Jul 2, 2018
ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how pro...
Protein Structure, Secondary Sequence Alignment Sequence Homology, Amino Acid Protein Interaction Domains and Motifs Escherichia coli Proteins Internet Amino Acid Sequence Structural Homology, Protein Humans Software Databases, Factual Deep Learning Computational Biology
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