AIMC Topic: Models, Molecular

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Protein structure modeling and refinement by global optimization in CASP12.

Proteins Dec 5, 2017
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...
Computational Biology Support Vector Machine Models, Statistical Proteins Humans Machine Learning Algorithms Protein Conformation Protein Folding Sequence Analysis, Protein Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray
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Assessment of the model refinement category in CASP12.

Proteins Nov 29, 2017
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the pre...
Humans Protein Folding Computational Biology Crystallography, X-Ray Sequence Analysis, Protein Proteins Machine Learning Protein Conformation Models, Molecular Algorithms
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Design of a calix[4]arene-functionalized metal-organic framework probe for highly sensitive and selective monitor of hippuric acid for indexing toluene exposure.

Analytica chimica acta Nov 23, 2017
In the present work, a novel metal-organic framework (MOF) fluorescent probe was prepared by post-synthetic modification of MIL-53-NH(Al) with carboxylatocalix[4]arene (CC[4]A). The introduced CC[4]A could not only enhance the fluorescence performanc...
Metal-Organic Frameworks Urinalysis Humans Models, Molecular Calixarenes Fluorescent Dyes Reagent Strips Limit of Detection Toluene Hippurates Phenols Spectrometry, Fluorescence
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B-factor profile prediction for RNA flexibility using support vector machines.

Journal of computational chemistry Nov 21, 2017
Determining the flexibility of structured biomolecules is important for understanding their biological functions. One quantitative measurement of flexibility is the atomic Debye-Waller factor or temperature B-factor. Most existing studies are limited...
RNA, Ribosomal Temperature Support Vector Machine Models, Molecular
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Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.

Proteins Nov 14, 2017
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successf...
Humans Machine Learning Databases, Protein Models, Molecular Crystallography, X-Ray Protein Conformation Algorithms Computational Biology Proteins Protein Folding Sequence Alignment Sequence Analysis, Protein
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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...
Crystallography, X-Ray Protein Conformation Protein Folding Sequence Alignment Humans Sequence Analysis, Protein Machine Learning Databases, Protein Algorithms Models, Molecular Datasets as Topic Computational Biology Proteins
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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...
Humans Machine Learning Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Algorithms Models, Molecular Computational Biology Molecular Dynamics Simulation Proteins Crystallography, X-Ray
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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 ...
Molecular Dynamics Simulation Amino Acid Sequence Intrinsically Disordered Proteins Calorimetry Circular Dichroism Thermodynamics Protein Folding Fuzzy Logic Models, Molecular Kinetics Protein Binding
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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,...
Models, Molecular Proteins Protein Conformation Machine Learning Structure-Activity Relationship 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 ...
Algorithms Computational Biology Proteins Neural Networks, Computer Machine Learning Software Protein Conformation Protein Interaction Domains and Motifs Humans Models, Molecular Internet Crystallography, X-Ray
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