AIMC Topic: Amino Acids

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Prediction of lysine propionylation sites using biased SVM and incorporating four different sequence features into Chou's PseAAC.

Journal of molecular graphics & modelling Jul 25, 2017
Lysine propionylation is an important and common protein acylation modification in both prokaryotes and eukaryotes. To better understand the molecular mechanism of propionylation, it is important to identify propionylated substrates and their corresp...
Reproducibility of Results Peptides Computational Biology Algorithms Support Vector Machine Protein Processing, Post-Translational Amino Acids Amino Acid Sequence Acetylation Lysine Position-Specific Scoring Matrices
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FFLUX: Transferability of polarizable machine-learned electrostatics in peptide chains.

Journal of computational chemistry Mar 10, 2017
The fully polarizable, multipolar, and atomistic force field protein FFLUX is being built from machine learning (i.e., kriging) models, each of which predicts an atomic property. Each atom of a given protein geometry needs to be assigned such a krigi...
Models, Theoretical Machine Learning Thermodynamics Proteins Physical Phenomena Peptides Amino Acids Models, Molecular Protein Conformation Static Electricity
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Toward amino acid typing for proteins in FFLUX.

Journal of computational chemistry Dec 19, 2016
Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic cha...
Machine Learning Computational Biology Proteins Quantum Theory Molecular Structure Amino Acids
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Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids.

International journal of molecular sciences Oct 26, 2016
Information about the interface sites of Protein-Protein Interactions (PPIs) is useful for many biological research works. However, despite the advancement of experimental techniques, the identification of PPI sites still remains as a challenging tas...
Protein Interaction Maps Proteins Databases, Protein Humans Machine Learning Animals Protein Interaction Mapping Protein Interaction Domains and Motifs Amino Acids Models, Biological Intrinsically Disordered Proteins
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Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks.

Bioinformatics (Oxford, England) Aug 22, 2016
MOTIVATION: Backbone structures and solvent accessible surface area of proteins are benefited from continuous real value prediction because it removes the arbitrariness of defining boundary between different secondary-structure and solvent-accessibil...
Neural Networks, Computer Computational Biology Solvents Protein Structure, Secondary Proteins Amino Acids
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Surface Adsorbed Antibody Characterization Using ToF-SIMS with Principal Component Analysis and Artificial Neural Networks.

Langmuir : the ACS journal of surfaces and colloids Aug 19, 2016
Artificial neural networks (ANNs) form a class of powerful multivariate analysis techniques, yet their routine use in the surface analysis community is limited. Principal component analysis (PCA) is more commonly employed to reduce the dimensionality...
Amino Acids Antibodies Multivariate Analysis ErbB Receptors Immunoglobulin Fragments Spectrometry, Mass, Secondary Ion Animals Adsorption Principal Component Analysis Humans Neural Networks, Computer Immunoglobulin G
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In Silico Prediction of Gamma-Aminobutyric Acid Type-A Receptors Using Novel Machine-Learning-Based SVM and GBDT Approaches.

BioMed research international Aug 8, 2016
Gamma-aminobutyric acid type-A receptors (GABAARs) belong to multisubunit membrane spanning ligand-gated ion channels (LGICs) which act as the principal mediators of rapid inhibitory synaptic transmission in the human brain. Therefore, the category p...
Receptors, GABA-A Computational Biology Models, Statistical Brain Amino Acids Support Vector Machine Humans Decision Trees Ligands Decision Making Computer Simulation Databases, Protein Machine Learning Amino Acid Motifs Reproducibility of Results Algorithms
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Prediction of fermentation index of cocoa beans (Theobroma cacao L.) based on color measurement and artificial neural networks.

Talanta Aug 5, 2016
Several procedures are currently used to assess fermentation index (FI) of cocoa beans (Theobroma cacao L.) for quality control. However, all of them present several drawbacks. The aim of the present work was to develop and validate a simple image ba...
Cacao Neural Networks, Computer Color Amino Acids Fermentation
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An improved method for predicting interactions between virus and human proteins.

Journal of bioinformatics and computational biology Jul 10, 2016
The interaction of virus proteins with host proteins plays a key role in viral infection and consequent pathogenesis. Many computational methods have been proposed to predict protein-protein interactions (PPIs), but most of the computational methods ...
Databases, Protein Amino Acids Hepacivirus Host-Pathogen Interactions Gene Ontology Protein Interaction Mapping Viral Proteins Reproducibility of Results Alphapapillomavirus Computational Biology Humans Support Vector Machine
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A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features.

Journal of bioinformatics and computational biology Jun 14, 2016
Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, orga...
Humans Machine Learning Amino Acids Support Vector Machine Protein Processing, Post-Translational Lipoylation Algorithms Proteins Databases, Protein Colorectal Neoplasms Computational Biology
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