AIMC Topic: Protein Conformation

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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 Machine Learning Crystallography, X-Ray Protein Conformation Protein Folding Sequence Analysis, Protein 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 Humans Protein Folding Algorithms Machine Learning Computational Biology Proteins Databases, Protein
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Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.

Journal of computer-aided molecular design Nov 13, 2017
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org...
Humans Neural Networks, Computer Machine Learning Molecular Docking Simulation Ligands Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Computer-Aided Design Drug Design Protein Binding Molecular Dynamics Simulation
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Specific and intrinsic sequence patterns extracted by deep learning from intra-protein binding and non-binding peptide fragments.

Scientific reports Nov 2, 2017
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins. Here we sh...
Protein Conformation Binding Sites Proteins Databases, Protein Algorithms Peptide Fragments Deep Learning Amino Acid Sequence Protein Binding
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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...
Proteins Databases, Protein Models, Molecular Datasets as Topic Sequence Analysis, Protein Humans Crystallography, X-Ray Protein Conformation Machine Learning Protein Folding Algorithms Sequence Alignment Computational Biology
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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 Algorithms Computational Biology Proteins Models, Molecular Humans Machine Learning
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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 Machine Learning Algorithms Proteins
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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 ...
Neural Networks, Computer Crystallography, X-Ray Machine Learning Protein Conformation Software Protein Interaction Domains and Motifs Computational Biology Humans Proteins Algorithms Models, Molecular Internet
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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...
Protein Multimerization Expert Systems Cattle Isoenzymes Mutagenesis, Site-Directed Biocatalysis Ubiquitin-Protein Ligases Computational Biology Point Mutation Models, Molecular Ubiquitin-Conjugating Enzymes Protein Conformation Iodine Radioisotopes Cysteine Amino Acid Substitution Recombinant Fusion Proteins Binding Sites Humans Animals Molecular Docking Simulation Ubiquitin Ubiquitination
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Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.

Journal of computer-aided molecular design Sep 18, 2017
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and ded...
Drug Design Ligands Protein Binding Protein Conformation Proteins Binding Sites Humans Databases, Protein Structure-Activity Relationship Machine Learning Molecular Structure Algorithms Knowledge Bases Molecular Docking Simulation
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