AI Medical Compendium Topic:
Protein Conformation

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Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Proteins Oct 26, 2017
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted resid...
Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray Protein Conformation Machine Learning Algorithms Computational Biology Proteins Sequence Analysis, Protein Protein Interaction Domains and Motifs Humans
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Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure.

Molecules (Basel, Switzerland) Oct 9, 2017
Protein structure and protein function should be related, yet the nature of this relationship remains unsolved. Mapping the critical residues for protein function with protein structure features represents an opportunity to explore this relationship,...
Proteins Structure-Activity Relationship Models, Molecular Protein Conformation Machine Learning Algorithms
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Improved protein contact predictions with the MetaPSICOV2 server in CASP12.

Proteins Sep 29, 2017
In this paper, we present the results for the MetaPSICOV2 contact prediction server in the CASP12 community experiment (http://predictioncenter.org). Over the 35 assessed Free Modelling target domains the MetaPSICOV2 server achieved a mean precision ...
Humans Computational Biology Proteins Models, Molecular Internet Neural Networks, Computer Machine Learning Software Algorithms Crystallography, X-Ray Protein Conformation Protein Interaction Domains and Motifs
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modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

The Journal of biological chemistry Sep 18, 2017
To understand the mechanism for assembly of Lys-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys...
Ubiquitin-Conjugating Enzymes Iodine Radioisotopes Expert Systems Ubiquitination Binding Sites Biocatalysis Protein Multimerization Molecular Docking Simulation Protein Conformation Mutagenesis, Site-Directed Isoenzymes Cattle Ubiquitin Point Mutation Computational Biology Cysteine Humans Ubiquitin-Protein Ligases Animals Amino Acid Substitution Models, Molecular Recombinant Fusion Proteins
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Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.

Journal of computer-aided molecular design Sep 18, 2017
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and ded...
Ligands Protein Conformation Binding Sites Databases, Protein Structure-Activity Relationship Molecular Structure Knowledge Bases Humans Molecular Docking Simulation Machine Learning Drug Design Algorithms Protein Binding Proteins
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Interaction prediction in structure-based virtual screening using deep learning.

Computers in biology and medicine Sep 14, 2017
We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each molecule separately. These f...
Deep Learning Proteins Databases, Protein Protein Conformation
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Analysis of deep learning methods for blind protein contact prediction in CASP12.

Proteins Sep 6, 2017
Here we present the results of protein contact prediction achieved in CASP12 by our RaptorX-Contact server, which is an early implementation of our deep learning method for contact prediction. On a set of 38 free-modeling target domains with a median...
Deep Learning Humans Computational Biology Neural Networks, Computer Proteins Crystallography, X-Ray Software Models, Molecular Protein Conformation Algorithms Protein Folding
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Elastic network model of learned maintained contacts to predict protein motion.

PloS one Aug 30, 2017
We present a novel elastic network model, lmcENM, to determine protein motion even for localized functional motions that involve substantial changes in the protein's contact topology. Existing elastic network models assume that the contact topology r...
Protein Conformation Arachidonate 15-Lipoxygenase Proteins Humans Models, Molecular Machine Learning Motion Animals Elasticity
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In silico identification of milk antihypertensive di- and tripeptides involved in angiotensin I-converting enzyme inhibitory activity.

Nutrition research (New York, N.Y.) Jul 28, 2017
Identification of bioactive milk peptides could improve food technology through improved selection of food supplements with a focus on antihypertensive properties. We hypothesized that angiotensin I-converting enzyme (ACE) inhibitory activities of mi...
Milk Proteins Dipeptides Hydrophobic and Hydrophilic Interactions Expert Systems Catalytic Domain Hydrogen Bonding Humans Molecular Docking Simulation Oligopeptides Peptidyl-Dipeptidase A Animals Antihypertensive Agents Cattle Angiotensin-Converting Enzyme Inhibitors Proteolysis Computational Biology Models, Molecular Quantitative Structure-Activity Relationship Binding Sites Dietary Supplements Peptide Fragments Protein Conformation
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Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4.

Journal of chemical information and modeling Jul 10, 2017
Bromodomain-containing protein 4 (BRD4) is implicated in the pathogenesis of a number of different cancers, inflammatory diseases and heart failure. Much effort has been dedicated toward discovering novel scaffold BRD4 inhibitors (BRD4is) with differ...
Cell Line Structure-Activity Relationship Drug Evaluation, Preclinical Molecular Targeted Therapy Molecular Docking Simulation Protein Conformation Drug Discovery Cell Cycle Proteins Humans Nuclear Proteins Machine Learning Transcription Factors
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