AIMC Topic: Protein Conformation

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New insights into the efficiency of thymol synergistic effect with p-cymene in inhibiting advanced glycation end products: A multi-way analysis based on spectroscopic and electrochemical methods in combination with molecular docking study.

Journal of pharmaceutical and biomedical analysis Dec 24, 2017
Protein glycation in the body is one of the main reasons of diabetes complications. The electrochemical studies on the inhibitory mechanism of glycation are rather scarce. Thus, it is important to investigate the role of electrochemistry in the glyca...
Binding Sites Spectrophotometry, Ultraviolet Cymenes Hypoglycemic Agents Molecular Docking Simulation Kinetics Thymol Protein Conformation Protein Processing, Post-Translational Protein Binding Drug Synergism Structure-Activity Relationship Lysine Glycosylation Monoterpenes Electrochemical Techniques Serum Albumin, Bovine Arginine Glycation End Products, Advanced
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Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.

Cell systems Dec 20, 2017
While genes are defined by sequence, in biological systems a protein's function is largely determined by its three-dimensional structure. Evolutionary information embedded within multiple sequence alignments provides a rich source of data for inferri...
Sequence Alignment Animals Computational Biology Proteins Neural Networks, Computer Databases, Protein Models, Molecular Machine Learning Humans Probability Algorithms Protein Conformation Forecasting Protein Folding
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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...
Algorithms Computational Biology Support Vector Machine Models, Statistical Humans Machine Learning Protein Conformation Protein Folding Sequence Analysis, Protein Proteins 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...
Proteins Models, Molecular Crystallography, X-Ray Protein Conformation Humans Machine Learning Algorithms Computational Biology Protein Folding Sequence Analysis, Protein
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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...
Protein Conformation Protein Folding Sequence Alignment Sequence Analysis, Protein Databases, Protein Models, Molecular Crystallography, X-Ray Humans Machine Learning Algorithms Computational Biology Proteins
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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...
Binding Sites Molecular Docking Simulation Computer-Aided Design Drug Design Protein Binding Molecular Dynamics Simulation Ligands Protein Conformation Receptors, Cytoplasmic and Nuclear Humans Neural Networks, Computer Machine Learning
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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...
Amino Acid Sequence Protein Conformation Binding Sites Protein Binding Proteins Databases, Protein Peptide Fragments Algorithms Deep Learning
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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...
Sequence Alignment Sequence Analysis, Protein Humans Machine Learning Datasets as Topic Algorithms Crystallography, X-Ray Protein Conformation Protein Folding Computational Biology Proteins Databases, Protein Models, Molecular
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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...
Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray Protein Conformation Sequence Analysis, Protein Humans Machine Learning Protein Interaction Domains and Motifs Algorithms Computational Biology Proteins
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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,...
Machine Learning Algorithms Protein Conformation Proteins Structure-Activity Relationship Models, Molecular
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