AIMC Topic: Sequence Alignment

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Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.

Proteins Nov 14, 2017
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successf...
Computational Biology Proteins Databases, Protein Humans Machine Learning Algorithms Protein Folding Sequence Alignment Sequence Analysis, Protein Models, Molecular Crystallography, X-Ray Protein Conformation
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Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

Proteins Oct 31, 2017
In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on co...
Humans Machine Learning Datasets as Topic Crystallography, X-Ray Proteins Protein Folding Protein Conformation Databases, Protein Algorithms Sequence Alignment Models, Molecular Computational Biology Sequence Analysis, Protein
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Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning.

Biochemistry Oct 26, 2017
As one of the most intrinsically reactive amino acids, cysteine carries a variety of important biochemical functions, including catalysis and redox regulation. Discovery and characterization of cysteines with heightened reactivity will help annotate ...
Proteomics Chromatography, Liquid Tandem Mass Spectrometry Decision Support Techniques Recombinant Proteins Amino Acid Motifs Escherichia coli Proteins Cysteine Sequence Alignment Humans Machine Learning
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NFPscanner: a webtool for knowledge-based deciphering of biomedical networks.

BMC bioinformatics May 18, 2017
BACKGROUND: Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics da...
Sequence Alignment Internet Knowledge Bases Software Algorithms Reproducibility of Results Gene Regulatory Networks Cluster Analysis
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A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition.

Journal of theoretical biology May 3, 2017
The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral metho...
Proteins Protein Folding Sequence Alignment Sequence Analysis, Protein Machine Learning Algorithms
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Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations.

IEEE/ACM transactions on computational biology and bioinformatics Apr 18, 2017
Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic...
Humans Animals Mice Computational Biology Proteins Sequence Analysis, Protein Molecular Sequence Annotation Databases, Protein Gene Ontology Amino Acid Sequence Sequence Alignment Semantics
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Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Journal of structural and functional genomics Jan 12, 2017
Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino ...
Computer Heuristics Algorithms Computational Biology Models, Molecular Sequence Alignment Proteins Sequence Analysis, Protein Databases, Protein
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SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity.

PloS one Aug 15, 2016
Knowledge of protein function is important for biological, medical and therapeutic studies, but many proteins are still unknown in function. There is a need for more improved functional prediction methods. Our SVM-Prot web-server employed a machine l...
Internet Amino Acid Sequence Sequence Alignment Proteins Databases, Protein Computational Biology Support Vector Machine
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Detecting false positive sequence homology: a machine learning approach.

BMC bioinformatics Feb 24, 2016
BACKGROUND: Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to ...
Sequence Homology Machine Learning False Positive Reactions Sequence Alignment
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Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

Bioinformatics (Oxford, England) Oct 29, 2015
MOTIVATION: Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to pep...
Algorithms Humans Sequence Alignment Peptide Fragments Neural Networks, Computer Protein Binding Epitopes Computational Biology Histocompatibility Antigens Class I
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