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Models, Molecular

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Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

Proteins Oct 31, 2017
In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on co...
Algorithms Computational Biology Proteins Databases, Protein Humans Machine Learning Protein Conformation Protein Folding Sequence Alignment Sequence Analysis, Protein Models, Molecular Datasets as Topic Crystallography, X-Ray
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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...
Crystallography, X-Ray Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Humans Machine Learning Algorithms Computational Biology Proteins Models, Molecular Molecular Dynamics Simulation
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The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein.

Angewandte Chemie (International ed. in English) Oct 10, 2017
Many intrinsically disordered proteins (IDP) that fold upon binding retain conformational heterogeneity in IDP-target complexes. The thermodynamics of such fuzzy interactions is poorly understood. Herein we introduce a thermodynamic framework, based ...
Protein Binding Fuzzy Logic Models, Molecular Kinetics Thermodynamics Molecular Dynamics Simulation Protein Folding Amino Acid Sequence Calorimetry Intrinsically Disordered Proteins Circular Dichroism
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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,...
Structure-Activity Relationship Models, Molecular Protein Conformation Algorithms Proteins Machine Learning
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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 ...
Crystallography, X-Ray Machine Learning Protein Conformation Humans Software Protein Interaction Domains and Motifs Neural Networks, Computer Algorithms Models, Molecular Computational Biology Internet 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...
Point Mutation Ubiquitin-Conjugating Enzymes Molecular Docking Simulation Ubiquitin Cattle Ubiquitination Computational Biology Protein Multimerization Models, Molecular Isoenzymes Recombinant Fusion Proteins Humans Binding Sites Animals Protein Conformation Mutagenesis, Site-Directed Ubiquitin-Protein Ligases Iodine Radioisotopes Cysteine Amino Acid Substitution Expert Systems Biocatalysis
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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...
Protein Folding Algorithms Deep Learning Computational Biology Crystallography, X-Ray Protein Conformation Proteins Humans Models, Molecular Neural Networks, Computer Software
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Identifying novel factor XIIa inhibitors with PCA-GA-SVM developed vHTS models.

European journal of medicinal chemistry Sep 1, 2017
There currently is renewed interest in blood clotting Factor XII as a potential target for thrombosis inhibition. Historically untargeted, there is little drug information with which to start drug candidate searches. Typical high-throughput screening...
Humans Dose-Response Relationship, Drug Blood Proteins Algorithms Support Vector Machine Molecular Structure Factor XIIa Structure-Activity Relationship Principal Component Analysis Models, Molecular
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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...
Proteins Elasticity Humans Models, Molecular Protein Conformation Machine Learning Motion Animals Arachidonate 15-Lipoxygenase
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Protein binding hot spots prediction from sequence only by a new ensemble learning method.

Amino acids Aug 1, 2017
UNLABELLED: Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods hav...
Sequence Analysis, Protein Machine Learning Algorithms Databases, Protein Models, Molecular
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