AIMC Topic: Protein Conformation

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A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

International journal of molecular sciences Jul 27, 2016
Understanding protein-protein interactions is a key challenge in biochemistry. In this work, we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein interfaces from their native complex structure compared to previous publ...
Humans Machine Learning Databases, Protein Protein Conformation Protein Interaction Mapping Protein Interaction Domains and Motifs Algorithms Computational Biology Proteins
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Protease Inhibitors in View of Peptide Substrate Databases.

Journal of chemical information and modeling Jun 9, 2016
Protease substrate profiling has nowadays almost become a routine task for experimentalists, and the knowledge on protease peptide substrates is easily accessible via the MEROPS database. We present a shape-based virtual screening workflow using vROC...
Peptides Databases, Pharmaceutical Machine Learning User-Computer Interface Protein Conformation Models, Molecular Protease Inhibitors Substrate Specificity Drug Evaluation, Preclinical Small Molecule Libraries Ligands Peptide Hydrolases
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Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.

Journal of chemical information and modeling May 20, 2016
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in vivo activity is more strongly correlated with the binding/unbind...
Drug Discovery Protein Binding Computational Biology Machine Learning Ligands Protein Conformation Static Electricity Thermodynamics Kinetics Molecular Dynamics Simulation Safety
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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...
Drug Evaluation, Preclinical Protein Conformation Machine Learning User-Computer Interface Molecular Dynamics Simulation
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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...
Cell Membrane Protein Conformation Protein Binding Supervised Machine Learning Ligands Receptors, G-Protein-Coupled Molecular Dynamics Simulation
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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...
Area Under Curve Ligands Crystallization Hydrogen Cathepsin K Protein Conformation Reproducibility of Results Chemistry, Pharmaceutical Drug Design Models, Statistical ROC Curve Binding Sites Proteins Imaging, Three-Dimensional Combinatorial Chemistry Techniques Databases, Protein Protein Binding Humans Computational Biology Software Support Vector Machine Algorithms
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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 ...
Protein Conformation Artificial Intelligence Peptides Proteome Humans Bacterial Proteins Bacillus subtilis HeLa Cells Chromatography, Liquid Quantitative Structure-Activity Relationship Tandem Mass Spectrometry Models, Chemical
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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...
Amino Acids Protein Conformation Support Vector Machine Proteins Models, Molecular Algorithms ROC Curve
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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...
Databases, Protein Neural Networks, Computer Protein Conformation Molecular Docking Simulation Proteins
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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...
Databases, Factual Protein Conformation Female Gene Ontology Knowledge Bases Comorbidity Humans Biochemical Phenomena Gene Regulatory Networks Polycystic Ovary Syndrome Databases, Chemical Polymorphism, Single Nucleotide Mutation
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