AI Medical Compendium Topic:
Protein Conformation

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Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability.

Molecules (Basel, Switzerland) Jan 27, 2018
Predicting how a point mutation alters a protein's stability can guide pharmaceutical drug design initiatives which aim to counter the effects of serious diseases. Conducting mutagenesis studies in physical proteins can give insights about the effect...
Protein Conformation Amino Acid Substitution Thermodynamics Decision Trees Proteins Mutation Protein Stability Neural Networks, Computer Computer Simulation Support Vector Machine
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Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition.

Journal of chemical information and modeling Jan 10, 2018
Inspired by natural language processing techniques, we here introduce Mol2vec, which is an unsupervised machine learning approach to learn vector representations of molecular substructures. Like the Word2vec models, where vectors of closely related w...
Algorithms Molecular Structure Models, Chemical Datasets as Topic Protein Conformation Reproducibility of Results Proteins Unsupervised Machine Learning Natural Language Processing
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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 Kinetics Molecular Docking Simulation Protein Conformation Hypoglycemic Agents Cymenes Drug Synergism Protein Binding Lysine Thymol Protein Processing, Post-Translational Monoterpenes Serum Albumin, Bovine Glycosylation Structure-Activity Relationship Arginine Glycation End Products, Advanced Electrochemical Techniques
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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...
Forecasting Animals Computational Biology Proteins Neural Networks, Computer Machine Learning Algorithms Protein Folding Sequence Alignment Databases, Protein Models, Molecular Probability Protein Conformation Humans
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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 Crystallography, X-Ray Models, Statistical Protein Interaction Domains and Motifs Protein Conformation Algorithms Proteins Protein Folding Models, Molecular Computational Biology Sequence Analysis, Protein Molecular Dynamics Simulation Support Vector Machine
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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 Models, Molecular Crystallography, X-Ray Protein Conformation Protein Folding Sequence Analysis, Protein Humans Machine Learning Algorithms
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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 Analysis, Protein Protein Conformation Protein Folding Sequence Alignment Humans Proteins Databases, Protein Machine Learning Models, Molecular Algorithms Crystallography, X-Ray Computational Biology
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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...
Drug Design Protein Binding Molecular Dynamics Simulation Ligands Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Neural Networks, Computer Machine Learning Molecular Docking Simulation Computer-Aided Design Humans
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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...
Algorithms Peptide Fragments Deep Learning Amino Acid Sequence Protein Conformation Protein Binding Binding Sites Proteins Databases, Protein
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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...
Humans Machine Learning Algorithms Datasets as Topic Sequence Alignment Crystallography, X-Ray Sequence Analysis, Protein Computational Biology Protein Conformation Proteins Protein Folding Databases, Protein Models, Molecular
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