AIMC Topic: Sequence Analysis, Protein

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Prediction of lysine glutarylation sites by maximum relevance minimum redundancy feature selection.

Analytical biochemistry Apr 8, 2018
Lysine glutarylation is new type of protein acylation modification in both prokaryotes and eukaryotes. To better understand the molecular mechanism of glutarylation, it is important to identify glutarylated substrates and their corresponding glutaryl...
Software Lysine Glutarates Sequence Analysis, Protein Acylation Support Vector Machine Protein Processing, Post-Translational Proteins
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The Impact of Protein Structure and Sequence Similarity on the Accuracy of Machine-Learning Scoring Functions for Binding Affinity Prediction.

Biomolecules Mar 14, 2018
It has recently been claimed that the outstanding performance of machine-learning scoring functions (SFs) is exclusively due to the presence of training complexes with highly similar proteins to those in the test set. Here, we revisit this question u...
Sequence Analysis, Protein Machine Learning Molecular Docking Simulation Protein Interaction Mapping
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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,...
Sequence Homology, Amino Acid Reproducibility of Results Sequence Analysis, Protein Protein Interaction Maps Protein Conformation Computational Biology Software Gene Ontology Internet Protein Interaction Mapping Proteins Algorithms Amino Acid Sequence Models, Molecular
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PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework.

Journal of theoretical biology Feb 1, 2018
Determining the catalytic residues in an enzyme is critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel enzymes and their inhibitors. Although many enzymes have been s...
Databases, Protein Catalysis Protein Conformation Sequence Analysis, Protein Machine Learning Software
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Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms.

Computational and mathematical methods in medicine Jan 30, 2018
We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs) and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or si...
Ligands False Positive Reactions Binding Sites Amino Acid Motifs Sequence Analysis, Protein Receptors, G-Protein-Coupled Area Under Curve Software Quercetin Algorithms Reproducibility of Results Humans ROC Curve Machine Learning Protein Binding
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iMem-2LSAAC: A two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into chou's pseudo amino acid composition.

Journal of theoretical biology Jan 11, 2018
Membrane proteins execute significant roles in cellular processes of living organisms, ranging from cell signaling to cell adhesion. As a major part of a cell, the identification of membrane proteins and their functional types become a challenging jo...
Support Vector Machine Databases, Protein Amino Acid Sequence Reproducibility of Results Computational Biology Membrane Proteins Sequence Analysis, Protein Neural Networks, Computer Algorithms
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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...
Software Algorithms Humans Neural Networks, Computer Sequence Homology, Amino Acid Amino Acid Motifs Sequence Analysis, Protein Support Vector Machine Proteins Databases, Factual Databases, Protein Reproducibility of Results Computational Biology
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Protein structure modeling and refinement by global optimization in CASP12.

Proteins Dec 5, 2017
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...
Protein Folding Sequence Analysis, Protein Protein Interaction Domains and Motifs Molecular Dynamics Simulation Crystallography, X-Ray Models, Statistical Machine Learning Protein Conformation Proteins Algorithms Computational Biology Humans Models, Molecular Support Vector Machine
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Assessment of the model refinement category in CASP12.

Proteins Nov 29, 2017
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the pre...
Models, Molecular Crystallography, X-Ray Protein Conformation Protein Folding Algorithms Humans Sequence Analysis, Protein Computational Biology Machine Learning Proteins
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Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.

Proteins Nov 29, 2017
Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and a database of GO term predic...
Models, Biological PTEN Phosphohydrolase Gene Ontology Transcriptome Humans Sequence Analysis, Protein Proteomics Machine Learning Databases, Protein Animals
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