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Protein Interaction Domains and Motifs

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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife 29927385
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Amino Acid Sequence Animals Binding Sites Crystallography, X-Ray Gene Expression Humans Kinetics Machine Learning Models, Molecular Point Mutation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Engineering Protein Interaction Domains and Motifs Protein Stability Receptor, Serotonin, 5-HT2C Sequence Alignment Sequence Homology, Amino Acid Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Thermodynamics
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Analysis of the Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach.

International journal of molecular sciences 31216622
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk facto...
Computational Biology Estrogen Receptor alpha Humans Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Mutation Neural Networks, Computer Polymorphism, Single Nucleotide Protein Binding Protein Conformation Protein Interaction Domains and Motifs Structure-Activity Relationship Tumor Suppressor Protein p53
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The PSIPRED Protein Analysis Workbench: 20 years on.

Nucleic acids research 31251384
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 year...
Amino Acid Sequence Binding Sites Gene Ontology History, 21st Century Internet Models, Molecular Molecular Sequence Annotation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Proteins Sequence Alignment Sequence Homology, Amino Acid Software
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research 31114883
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...
Benchmarking Binding Sites Crystallography, X-Ray Datasets as Topic Humans Internet Machine Learning Mutation, Missense Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Proteins Software Thermodynamics
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PrankWeb: a web server for ligand binding site prediction and visualization.

Nucleic acids research 31114880
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability cent...
Amino Acid Sequence Benchmarking Binding Sites Datasets as Topic Humans Internet Ligands Machine Learning Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Proteins Software Thermodynamics
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Protein-protein interaction site prediction through combining local and global features with deep neural networks.

Bioinformatics (Oxford, England) 31593229
MOTIVATION: Protein-protein interactions (PPIs) play important roles in many biological processes. Conventional biological experiments for identifying PPI sites are costly and time-consuming. Thus, many computational approaches have been proposed to ...
Amino Acid Sequence Neural Networks, Computer Protein Interaction Domains and Motifs Proteins Software
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Sequence-Based Prediction of Fuzzy Protein Interactions.

Journal of molecular biology 32112804
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...
Algorithms Amino Acid Sequence Databases, Protein Fuzzy Logic Humans Intrinsically Disordered Proteins Models, Molecular Protein Binding Protein Conformation Protein Domains Protein Folding Protein Interaction Domains and Motifs Sequence Analysis, Protein Sequence Homology
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Computational Identification and Analysis of Ubiquinone-Binding Proteins.

Cells 32102444
Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will...
Amino Acid Sequence Binding Sites Carrier Proteins Computational Biology Gene Ontology Humans Machine Learning Membrane Proteins Position-Specific Scoring Matrices Protein Binding Protein Interaction Domains and Motifs Sequence Analysis, Protein Ubiquinone
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Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning Approaches.

International journal of molecular sciences 32102234
Glucose-6-Phosphate Dehydrogenase (G6PD) is a ubiquitous cytoplasmic enzyme converting glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway (PPP). The G6PD deficiency renders the inability to regenerate glutathione due to lack...
Animals Catalytic Domain Drug Discovery Drug Evaluation, Preclinical Glucosephosphate Dehydrogenase Glucosephosphate Dehydrogenase Deficiency Glutathione Humans Machine Learning Molecular Docking Simulation NADP Oxidation-Reduction Oxidative Stress Pentose Phosphate Pathway Protein Interaction Domains and Motifs X-Ray Diffraction
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Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.

Scientific reports 32047225
Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational...
Animals Ants Gene Ontology Gene Regulatory Networks Genome, Insect Insect Proteins Molecular Sequence Annotation Protein Interaction Domains and Motifs Protein Interaction Maps Proteome
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