Research graph
References from InteracTor: Feature engineering and explainable AI for profiling protein structure-interaction-function relationships. Local targets link to admitted publications; unresolved targets remain external evidence.
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
10.1093/nar/gkab1061 · 2022 · External reference
Accurate prediction of protein structures and interactions using a three-track neural network
10.1126/science.abj8754 · 2021 · External reference
ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning
10.1093/bib/bbac031 · 2022 · External reference
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins
10.1093/bioinformatics/btz629 · 2020 · External reference
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy
10.1002/prot.24928 · 2015 · External reference
An updated dataset and a structure-based prediction model for protein-RNA binding affinity
10.1002/prot.26503 · 2023 · External reference
DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein-Ligand Interaction Prediction
10.3390/molecules28124691 · 2023 · External reference
3D deep convolutional neural networks for amino acid environment similarity analysis
10.1186/s12859-017-1702-0 · 2017 · External reference
Discovery of novel gain-of-function mutations guided by structure-based deep learning
10.1021/acssynbio.0c00345 · 2020 · External reference
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
10.1093/nar/gkac351 · 2022 · External reference
Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models
10.1089/cmb.2022.0241 · 2023 · External reference
ProFeatX: A parallelized protein feature extraction suite for machine learning
10.1016/j.csbj.2022.12.044 · 2022 · External reference
Interpreting Black-Box Models: A Review on Explainable Artificial Intelligence
10.1007/s12559-023-10179-8 · 2024 · External reference
Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins
10.1038/nsmb.1610 · 2009 · External reference
Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity
10.1016/j.biochi.2007.07.020 · 2007 · External reference
Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity
10.6026/97320630013164 · 2017 · External reference
Rama: a machine learning approach for ribosomal protein prediction in plants
10.1038/s41598-017-16322-4 · 2017 · External reference
RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors
10.3390/ijms232012176 · 2022 · External reference
Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae
10.1186/s12859-017-1839-x · 2017 · External reference
From Local Explanations to Global Understanding with Explainable AI for Trees
10.1038/s42256-019-0138-9 · 2020 · External reference
Contribution of hydrophobic interactions to protein stability
10.1016/j.jmb.2011.02.053 · 2011 · External reference
Peptide folding driven by Van der Waals interactions
10.1002/pro.2710 · 2015 · External reference
Protein Mechanics: A New Frontier in Biomechanics
10.1007/s11340-008-9154-0 · 2009 · External reference
Hydrogen bonds: simple after all?
10.1021/acs.biochem.8b00217 · 2018 · External reference
Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model
10.1021/acs.jpcb.8b02814 · 2018 · External reference
How sticky are our proteins? Quantifying hydrophobicity of the human proteome
2022 · External reference
The Role of Protein Structure in Surface Tension Kinetics.
10.1007/978-94-011-3780-5_38 · 1990 · External reference
Dispersion Forces and the Molecular Origin of Internal Friction in Protein
10.1021/acs.biochem.6b00500 · 2016 · External reference
Environment and exposure to solvent of protein atoms. Lysozyme and insulin
10.1016/0022-2836(73)90011-9 · 1973 · External reference
Gene Ontology: Pitfalls, Biases, and Remedies.
10.1007/978-1-4939-3743-1_14 · 2017 · External reference
Protein sequence classification with improved extreme learning machine algorithms
2014 · External reference
Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics
10.1126/science.abf8761 · 2021 · External reference
The molecular basis for cellular function of intrinsically disordered protein regions
10.1038/s41580-023-00673-0 · 2024 · External reference
Emerging methods in protein co-evolution
10.1038/nrg3414 · 2013 · External reference
Synthesis and Biological Activity of N-Sulfonyltripeptides with C-Terminal Arginine as Potential Serine Proteases Inhibitors
10.1007/s10989-012-9338-4 · 2013 · External reference
Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures
10.1021/jp207807a · 2012 · External reference
Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets
10.1186/s13068-021-01964-4 · 2021 · External reference
Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
10.1006/jmbi.2001.4526 · 2001 · External reference
Engineering stringent genetic biocontainment of yeast with a protein stability switch
10.1038/s41467-024-44988-8 · 2024 · External reference
Proteins of unknown function in the protein data bank (PDB): An inventory of true uncharacterized proteins and computational tools for their analysis
10.3390/ijms131012761 · 2012 · External reference
Quantum Computing in the Next-Generation Computational Biology Landscape: From Protein Folding to Molecular Dynamics
10.1007/s12033-023-00765-4 · 2024 · External reference
Bisphosphonate conjugation enhances the bone-specificity of NELL-1-based systemic therapy for spaceflight-induced bone loss in mice
10.1038/s41526-023-00319-7 · 2023 · External reference
A perspective on protein structure prediction using quantum computers
10.1021/acs.jctc.4c00067 · 2024 · External reference
Towards synthetic biological approaches to resource utilization on space missions
10.1098/rsif.2014.0715 · 2015 · External reference
New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics
10.1093/bib/bbae074 · 2024 · External reference
A guide to machine learning for biologists
10.1038/s41580-021-00407-0 · 2022 · External reference
Machine learning approaches and their current application in plant molecular biology: A systematic review
10.1016/j.plantsci.2019.03.020 · 2019 · External reference
Competition of van der Waals and chemical forces on gold–sulfur surfaces and nanoparticles
10.1038/s41570-017-0017 · 2017 · External reference
Structural and biophysical characterization of human cytochromes P450 2B6 and 2A6 bound to volatile hydrocarbons: analysis and comparison
10.1124/mol.114.097014 · 2015 · External reference
Cytochrome P450 organization and function are modulated by endoplasmic reticulum phospholipid heterogeneity
10.1124/dmd.115.068981 · 2016 · External reference
The Short-chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family
10.1002/prot.25666 · 2019 · External reference
Genome-Wide Identification and Characterization of Short-Chain Dehydrogenase/Reductase (SDR) Gene Family in Medicago truncatula
10.3390/ijms22179498 · 2021 · External reference
The structural basis for catalysis and specificity of the X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis
10.1016/s0969-2126(02)00851-1 · 2002 · External reference
Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes
10.1007/s00018-008-8588-y · 2008 · External reference
SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species
10.7554/elife.73913 · 2022 · External reference
Uncovering the Role of Hydrophobic Residues in Cytochrome P450−Cytochrome P450 Reductase Interactions
10.1021/bi1020748 · 2011 · External reference
Ligand access channels in cytochrome P450 enzymes: A review
10.3390/ijms19061617 · 2018 · External reference
The Repertoire of Solute-Binding Proteins of Model Bacteria Reveals Large Differences in Number, Type, and Ligand Range
10.1128/spectrum.02054-22 · 2022 · External reference
Pores, Channels and Transporters.
10.1007/978-1-4757-2065-5_8 · 1989 · External reference
Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer’s amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities
10.1002/pro.5560060902 · 1997 · External reference
Identification of protease serine S1 family member 53 as a mitochondrial protein in murine islet beta cells
10.1080/19382014.2021.1982325 · 2022 · External reference
Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion. Robinson NP, editor
10.1042/etls20180094 · 2018 · External reference
Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon
10.1126/science.1164748 · 2009 · External reference
The PDB_REDO server for macromolecular structure model optimization
10.1107/s2052252514009324 · 2014 · External reference
Open Babel: An open chemical toolbox
10.1186/1758-2946-3-33 · 2011 · External reference
UniProt: the universal protein knowledgebase in 2021
10.1093/nar/gkaa1100 · 2021 · External reference
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
10.1038/75556 · 2000 · External reference
The Protein Data Bank
10.1093/nar/28.1.235 · 2000 · External reference
Estimating mutual information
10.1103/physreve.69.066138 · 2004 · External reference
Principal component analysis: a review and recent developments
10.1098/rsta.2015.0202 · 2016 · External reference
Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
10.1038/s41467-019-13055-y · 2019 · External reference
Unresolved reference
External reference
FreeViz--an intelligent multivariate visualization approach to explorative analysis of biomedical data
10.1016/j.jbi.2007.03.010 · 2007 · External reference
Scikit-learn: Machine Learning in Python [Internet]
2018 · External reference
A Unified Approach to Interpreting Model Predictions [Internet]
2017 · External reference
Power analysis, sample size, and assessment of statistical assumptions—improving the evidential value of lighting research
10.1080/15502724.2018.1533851 · 2019 · External reference
Wilcoxon-Signed-Rank Test.
10.1007/978-3-642-04898-2_616 · 2011 · External reference
Multiple comparison test by Tukey’s honestly significant difference (HSD): Do the confident level control type I error
10.22271/maths.2021.v6.i1a.636 · 2021 · External reference
