AI Medical Compendium Topic:
Models, Molecular

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Binding Activity Prediction of Cyclin-Dependent Inhibitors.

Journal of chemical information and modeling Jul 10, 2015
The Cyclin-Dependent Kinases (CDKs) are the core components coordinating eukaryotic cell division cycle. Generally the crystal structure of CDKs provides information on possible molecular mechanisms of ligand binding. However, reliable and robust est...
Algorithms Protein Binding Support Vector Machine Machine Learning Protein Conformation Protein Kinase Inhibitors Chromosomes Cyclin-Dependent Kinases Decision Trees Models, Molecular Bayes Theorem
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SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets.

Structure (London, England : 1993) Jul 9, 2015
Identifying dynamical, quasi-rigid domains in proteins provides a powerful means for characterizing functionally oriented structural changes via a parsimonious set of degrees of freedom. In fact, the relative displacements of few dynamical domains us...
Adenylate Kinase Tobacco mosaic satellite virus Models, Molecular Internet Software Thermodynamics Multifactor Dimensionality Reduction Protein Structure, Tertiary Escherichia coli Ion Channels Capsid
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Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

Scientific reports Jun 22, 2015
Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independentl...
Models, Molecular Amino Acids Solvents Protein Structure, Secondary Algorithms Proteins Databases, Protein Machine Learning
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Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism.

BMC bioinformatics Jun 6, 2015
BACKGROUND: People with an autistic spectrum disorder (ASD) display a variety of characteristic behavioral traits, including impaired social interaction, communication difficulties and repetitive behavior. This complex neurodevelopment disorder is kn...
Nerve Tissue Proteins Models, Molecular High-Throughput Nucleotide Sequencing Mice Genomics Rats Genome Calcium-Binding Proteins Social Behavior Membrane Potentials Synapses Autistic Disorder Gene Ontology Phenotype Animals Synaptic Potentials Humans Cell Physiological Phenomena Cell Adhesion Molecules, Neuronal Neural Cell Adhesion Molecules
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Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

Acta crystallographica. Section D, Biological crystallography Apr 25, 2015
In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific know...
Algorithms Support Vector Machine Models, Molecular Zinc Metals Protein Conformation Macromolecular Substances Iron Manganese Nickel Crystallography, X-Ray Calcium
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In silico prediction of anti-malarial hit molecules based on machine learning methods.

International journal of computational biology and drug design Apr 13, 2015
Machine learning techniques have been widely used in drug discovery and development in the areas of cheminformatics. Aspartyl aminopeptidase (M18AAP) of Plasmodium falciparum is crucial for survival of malaria parasite. We have created predictive mod...
Models, Statistical Artificial Intelligence Models, Molecular Computer Simulation Antimalarials Drug Discovery
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All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Proceedings of the National Academy of Sciences of the United States of America Apr 9, 2015
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-hel...
Protein Structure, Tertiary Sequence Analysis, Protein Artificial Intelligence Escherichia coli Protein Structure, Secondary Receptors, Cell Surface Models, Molecular Escherichia coli Proteins
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Prediction of overall in vitro microsomal stability of drug candidates based on molecular modeling and support vector machines. Case study of novel arylpiperazines derivatives.

PloS one Mar 31, 2015
Other than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach i...
Support Vector Machine Microsomes Chromatography, Liquid Models, Molecular Spectrometry, Mass, Electrospray Ionization Piperazines Half-Life Tandem Mass Spectrometry
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Improved feature-based prediction of SNPs in human cytochrome P450 enzymes.

Interdisciplinary sciences, computational life sciences Mar 21, 2015
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...
Cytochrome P-450 Enzyme System Phylogeny Base Sequence Polymorphism, Single Nucleotide Codon Models, Molecular Computational Biology Humans Mutation Artificial Intelligence Support Vector Machine Amino Acids Amino Acid Sequence Fuzzy Logic Area Under Curve
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Recursive Random Forests Enable Better Predictive Performance and Model Interpretation than Variable Selection by LASSO.

Journal of chemical information and modeling Mar 16, 2015
Variable selection is of crucial significance in QSAR modeling since it increases the model predictive ability and reduces noise. The selection of the right variables is far more complicated than the development of predictive models. In this study, e...
Quantitative Structure-Activity Relationship Endpoint Determination Humans Machine Learning Models, Molecular
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