AIMC Topic: Protein Conformation

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Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.

Journal of chemical information and modeling May 3, 2016
Ensemble docking can be a successful virtual screening technique that addresses the innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method to identify a subset of conformational states that effectively segregates ac...
Molecular Dynamics Simulation Drug Evaluation, Preclinical Protein Conformation Machine Learning User-Computer Interface
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Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations.

Journal of chemical information and modeling Apr 14, 2016
Molecular recognition is a crucial issue when aiming to interpret the mechanism of known active substances as well as to develop novel active candidates. Unfortunately, simulating the binding process is still a challenging task because it requires cl...
Supervised Machine Learning Ligands Cell Membrane Protein Binding Receptors, G-Protein-Coupled Molecular Dynamics Simulation Protein Conformation
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The Virtual Screening of the Drug Protein with a Few Crystal Structures Based on the Adaboost-SVM.

Computational and mathematical methods in medicine Apr 3, 2016
Using the theory of machine learning to assist the virtual screening (VS) has been an effective plan. However, the quality of the training set may reduce because of mixing with the wrong docking poses and it will affect the screening efficiencies. To...
Binding Sites Combinatorial Chemistry Techniques Chemistry, Pharmaceutical Hydrogen Cathepsin K Proteins Databases, Protein Area Under Curve Ligands Crystallization Protein Conformation Computational Biology Support Vector Machine Models, Statistical Imaging, Three-Dimensional Protein Binding Humans Software Algorithms Reproducibility of Results Drug Design ROC Curve
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Exploiting non-linear relationships between retention time and molecular structure of peptides originating from proteomes and comparing three multivariate approaches.

Journal of pharmaceutical and biomedical analysis Jan 27, 2016
Peptides' retention time prediction is gaining increasing popularity in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics. This is a promising approach for improving successful proteome mapping, useful both in identification ...
Humans Bacillus subtilis Chromatography, Liquid Models, Chemical Artificial Intelligence Peptides Proteome Bacterial Proteins Quantitative Structure-Activity Relationship Tandem Mass Spectrometry Protein Conformation HeLa Cells
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Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11.

Scientific reports Jan 14, 2016
Quality assessment of a protein model is to predict the absolute or relative quality of a protein model using computational methods before the native structure is available. Single-model methods only need one model as input and can predict the absolu...
ROC Curve Support Vector Machine Proteins Models, Molecular Amino Acids Protein Conformation Algorithms
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Accurate refinement of docked protein complexes using evolutionary information and deep learning.

Journal of bioinformatics and computational biology Nov 24, 2015
One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes a...
Proteins Databases, Protein Protein Conformation Neural Networks, Computer Molecular Docking Simulation
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PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome.

Nucleic acids research Nov 17, 2015
Polycystic ovary syndrome (PCOS) is one of the major causes of female subfertility worldwide and ≈ 7-10% of women in reproductive age are affected by it. The affected individuals exhibit varying types and levels of comorbid conditions, along with the...
Biochemical Phenomena Databases, Chemical Protein Conformation Gene Ontology Mutation Knowledge Bases Comorbidity Polycystic Ovary Syndrome Gene Regulatory Networks Polymorphism, Single Nucleotide Humans Databases, Factual Female
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Prediction of Protein-Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures.

The Journal of membrane biology Nov 12, 2015
Accurately predicting protein-protein interaction sites (PPIs) is currently a hot topic because it has been demonstrated to be very useful for understanding disease mechanisms and designing drugs. Machine-learning-based computational approaches have ...
Machine Learning Reproducibility of Results Protein Binding Computational Biology Proteins Protein Conformation Binding Sites Protein Interaction Mapping Databases, Protein Models, Molecular Workflow
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Protein folds recognized by an intelligent predictor based-on evolutionary and structural information.

Journal of computational chemistry Oct 27, 2015
Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks inc...
Proteins Protein Conformation Protein Folding Neural Networks, Computer Computational Biology Evolution, Molecular
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APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction.

Computational biology and chemistry Sep 5, 2015
Tertiary protein structure prediction is one of the most challenging problems in structural bioinformatics. Despite the advances in algorithm development and computational strategies, predicting the folded structure of a protein only from its amino a...
Algorithms Knowledge Bases Computational Biology Proteins Protein Conformation Protein Structure, Tertiary
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