AIMC Topic: Protein Conformation

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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 ...
Protein Interaction Domains and Motifs Models, Molecular Internet Crystallography, X-Ray Protein Conformation Humans Neural Networks, Computer Machine Learning Software Algorithms Computational Biology Proteins
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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 Ubiquitination Protein Multimerization Isoenzymes Amino Acid Substitution Recombinant Fusion Proteins Binding Sites Mutagenesis, Site-Directed Point Mutation Ubiquitin-Conjugating Enzymes Computational Biology Models, Molecular Iodine Radioisotopes Expert Systems Biocatalysis Protein Conformation Cysteine Ubiquitin-Protein Ligases Humans Animals Molecular Docking Simulation Cattle
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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...
Algorithms Molecular Docking Simulation Drug Design Protein Binding Humans Machine Learning Binding Sites Molecular Structure Proteins Knowledge Bases Databases, Protein Ligands Structure-Activity Relationship Protein Conformation
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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...
Proteins Databases, Protein Protein Conformation Deep Learning
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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...
Humans Neural Networks, Computer Software Models, Molecular Crystallography, X-Ray Protein Conformation Algorithms Protein Folding Deep Learning Computational Biology Proteins
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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 Humans Arachidonate 15-Lipoxygenase Proteins Machine Learning Models, Molecular Animals Motion 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...
Expert Systems Catalytic Domain Oligopeptides Angiotensin-Converting Enzyme Inhibitors Quantitative Structure-Activity Relationship Humans Protein Conformation Animals Hydrogen Bonding Molecular Docking Simulation Peptidyl-Dipeptidase A Cattle Proteolysis Computational Biology Models, Molecular Binding Sites Dietary Supplements Peptide Fragments Milk Proteins Antihypertensive Agents Dipeptides Hydrophobic and Hydrophilic Interactions
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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...
Transcription Factors Machine Learning Molecular Targeted Therapy Cell Line Molecular Docking Simulation Humans Protein Conformation Structure-Activity Relationship Drug Discovery Cell Cycle Proteins Drug Evaluation, Preclinical Nuclear Proteins
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Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

Scientific reports Jun 16, 2017
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are impo...
Machine Learning Protein Interaction Maps Oxidation-Reduction Molecular Dynamics Simulation Protein Conformation Humans Protein Interaction Mapping Protein Disulfide-Isomerases Protein Interaction Domains and Motifs
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Protein-Protein Interaction Interface Residue Pair Prediction Based on Deep Learning Architecture.

IEEE/ACM transactions on computational biology and bioinformatics May 19, 2017
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interactio...
Protein Conformation Molecular Docking Simulation Binding Sites Deep Learning Protein Binding Computational Biology Proteins Surface Properties
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