AIMC Topic: Crystallography, X-Ray

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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Crystallography, X-Ray Binding Sites Protein Engineering Thermodynamics Kinetics Amino Acid Sequence Protein Stability Receptor, Serotonin, 5-HT2C Humans Protein Conformation, beta-Strand Machine Learning Sequence Alignment Point Mutation Animals Sequence Homology, Amino Acid Serotonin 5-HT2 Receptor Agonists Protein Binding Protein Interaction Domains and Motifs Serotonin 5-HT2 Receptor Antagonists Models, Molecular Protein Conformation, alpha-Helical Gene Expression
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Classification of crystallization outcomes using deep convolutional neural networks.

PloS one Jun 20, 2018
The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algori...
Crystallization Crystallography, X-Ray Neural Networks, Computer Algorithms Image Processing, Computer-Assisted Datasets as Topic
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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...
Humans Machine Learning Algorithms Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray Protein Conformation Computational Biology Support Vector Machine Models, Statistical Proteins Protein Folding Sequence Analysis, Protein Protein Interaction Domains and Motifs
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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...
Sequence Analysis, Protein Crystallography, X-Ray Protein Conformation Protein Folding Humans Machine Learning Algorithms Computational Biology Proteins 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...
Sequence Alignment Sequence Analysis, Protein Models, Molecular Crystallography, X-Ray Protein Conformation Protein Folding Computational Biology Proteins Databases, Protein Humans Machine Learning Algorithms
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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...
Computational Biology Proteins Databases, Protein Models, Molecular Humans Datasets as Topic Crystallography, X-Ray Machine Learning Sequence Alignment Protein Conformation Algorithms Sequence Analysis, Protein Protein Folding
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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...
Molecular Dynamics Simulation Crystallography, X-Ray Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Humans Algorithms Machine Learning Computational Biology Proteins Models, Molecular
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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 ...
Models, Molecular Humans Internet Protein Interaction Domains and Motifs Algorithms Neural Networks, Computer Crystallography, X-Ray Computational Biology Machine Learning Protein Conformation Proteins Software
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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 Models, Molecular Deep Learning Crystallography, X-Ray Computational Biology Protein Conformation Proteins Humans Neural Networks, Computer Software
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Learning the Relationship between the Primary Structure of HIV Envelope Glycoproteins and Neutralization Activity of Particular Antibodies by Using Artificial Neural Networks.

International journal of molecular sciences Oct 11, 2016
The dependency between the primary structure of HIV envelope glycoproteins (ENV) and the neutralization data for given antibodies is very complicated and depends on a large number of factors, such as the binding affinity of a given antibody for a giv...
Inhibitory Concentration 50 Databases, Protein Humans Crystallography, X-Ray Models, Molecular Magnetic Resonance Spectroscopy Neural Networks, Computer Antibodies, Neutralizing HIV Envelope Protein gp120 HIV Infections HIV-1
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