AIMC Topic: Crystallography, X-Ray

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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 Protein Conformation Machine Learning Algorithms Protein Folding Models, Molecular Sequence Analysis, Protein Molecular Dynamics Simulation Protein Interaction Domains and Motifs 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...
Computational Biology Proteins Humans Models, Molecular Machine Learning Protein Folding Crystallography, X-Ray Algorithms Sequence Analysis, Protein Protein Conformation
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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 Proteins Databases, Protein Models, Molecular Crystallography, X-Ray Machine Learning Algorithms Computational Biology Sequence Analysis, Protein Protein Conformation Protein Folding Sequence Alignment
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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...
Datasets as Topic Sequence Alignment Sequence Analysis, Protein Crystallography, X-Ray Protein Conformation Algorithms Protein Folding Computational Biology Proteins Humans Databases, Protein Models, Molecular Machine Learning
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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...
Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray Humans Computational Biology Proteins 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 ...
Proteins Models, Molecular Internet Protein Interaction Domains and Motifs Crystallography, X-Ray Protein Conformation Machine Learning Software Algorithms Computational Biology Humans Neural Networks, Computer
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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 Crystallography, X-Ray Protein Conformation Deep Learning Protein Folding Proteins Computational Biology Neural Networks, Computer Models, Molecular Software Algorithms
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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...
HIV Envelope Protein gp120 Humans HIV-1 Neural Networks, Computer Inhibitory Concentration 50 HIV Infections Databases, Protein Crystallography, X-Ray Models, Molecular Magnetic Resonance Spectroscopy Antibodies, Neutralizing
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Structure-activity relationship studies of 1-(1'-hydroxyalkyl)rupestonic acid methyl esters against influenza viruses.

Bioorganic & medicinal chemistry letters Jun 6, 2016
A series of 1-(1'-hydroxyalkyl)rupestonic acid methyl esters were synthesized via the condensation of methyl rupestonate with various aldehydes in the presence of LDA. This mixed aldol reaction was highly stereoselective and all the new compounds wer...
Azulenes Esters Orthomyxoviridae Sesquiterpenes Microbial Sensitivity Tests Crystallography, X-Ray Antiviral Agents Structure-Activity Relationship
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Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries.

Journal of chemical information and modeling May 24, 2016
Virtual screening consists of docking libraries of small molecules to a target protein followed by rank-ordering of the resulting structures using scoring functions. The ability of scoring methods to distinguish between actives and inactives depends ...
Small Molecule Libraries Protein Kinases Molecular Docking Simulation Support Vector Machine Ligands User-Computer Interface Drug Evaluation, Preclinical Crystallography, X-Ray Protein Binding
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