AI Medical Compendium Journal:
Proteins

Showing 71 to 80 of 82 articles

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 Humans Models, Molecular Neural Networks, Computer Internet Machine Learning Crystallography, X-Ray Software Protein Conformation Algorithms Computational Biology Proteins
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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 Protein Folding Algorithms Deep Learning Computational Biology Proteins
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Predicting the helix-helix interactions from correlated residue mutations.

Proteins Aug 24, 2017
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins. In spite of remarkable progresses over the past decades, the accuracy of predicting protein structures fro...
Membrane Proteins Amino Acid Sequence Protein Conformation, alpha-Helical Binding Sites Machine Learning Protein Interaction Domains and Motifs Protein Binding Computational Biology
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InterPred: A pipeline to identify and model protein-protein interactions.

Proteins Mar 21, 2017
Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the numb...
Protein Interaction Domains and Motifs Benchmarking Amino Acid Sequence Protein Interaction Mapping Sequence Analysis, Protein Software Molecular Docking Simulation Computational Biology Support Vector Machine Proteins Internet
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Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.

Proteins Mar 21, 2017
Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during t...
Software Computational Biology Support Vector Machine Benchmarking Molecular Dynamics Simulation Protein Conformation Monte Carlo Method Models, Statistical Proteins Double-Blind Method Internet
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A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.

Proteins Jan 20, 2017
Reliable identification of near-native poses of docked protein-protein complexes is still an unsolved problem. The intrinsic heterogeneity of protein-protein interactions is challenging for traditional biophysical or knowledge based potentials and th...
Protein Interaction Mapping Structural Homology, Protein Benchmarking Protein Conformation Binding Sites Thermodynamics Computational Biology Cluster Analysis Proteins Machine Learning Software Research Design Molecular Docking Simulation Protein Binding
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Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.

Proteins Dec 5, 2016
Predicting protein conformational changes from unbound structures or even homology models to bound structures remains a critical challenge for protein docking. Here we present a study directly addressing the challenge by reducing the dimensionality a...
Machine Learning Software Research Design Molecular Docking Simulation Thermodynamics Protein Multimerization Structural Homology, Protein Protein Binding Benchmarking Computational Biology Protein Conformation Models, Statistical Dimensional Measurement Accuracy Proteins Binding Sites
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TMSEG: Novel prediction of transmembrane helices.

Proteins Sep 16, 2016
Transmembrane proteins (TMPs) are important drug targets because they are essential for signaling, regulation, and transport. Despite important breakthroughs, experimental structure determination remains challenging for TMPs. Various methods have bri...
Databases, Protein Hydrophobic and Hydrophilic Interactions Datasets as Topic Protein Conformation, alpha-Helical Humans Machine Learning Sensitivity and Specificity Membrane Proteins
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GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

Proteins Jun 8, 2016
G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Protein Structure, Secondary Protein Multimerization Humans Protein Interaction Domains and Motifs Animals Area Under Curve ROC Curve Mice Models, Molecular Protein Binding Support Vector Machine Amino Acid Sequence Databases, Protein Binding Sites Receptors, G-Protein-Coupled
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Accurate contact predictions using covariation techniques and machine learning.

Proteins Aug 14, 2015
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Protein Folding Models, Statistical Software Humans Sequence Alignment Internet Proteins Neural Networks, Computer Protein Interaction Domains and Motifs Databases, Protein Computer Simulation Amino Acid Sequence Machine Learning Bacteria Models, Molecular Viruses Computational Biology Protein Structure, Secondary
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