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Using machine learning to predict quantitative phenotypes from protein and nucleic acid sequences
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Isolation of superoxide dismutase mutants in Escherichia coli: is superoxide dismutase necessary for aerobic life?
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Error Detecting and Error Correcting Codes
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Discrimination of mesophilic and thermophilic proteins using machine learning algorithms
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Thermodynamics of the unfolding of the cold-shock protein from Thermotoga maritima 1 1Edited by A. R. Fersht
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Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein 1 1Edited by D. C. Rees
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Approximation capabilities of multilayer feedforward networks
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Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins
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Dynamical properties of cold shock protein A from Mycobacterium tuberculosis
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Structure and flexibility of the thermophilic cold-shock protein of Thermus aquaticus
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Rapid Bioinformatic Identification of Thermostabilizing Mutations
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Machine Learning for Prioritization of Thermostabilizing Mutations for G-Protein Coupled Receptors
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The Folding Transition State of the Cold Shock Protein is Strongly Polarized
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Stabilization of the Cold Shock Protein CspB from Bacillus subtilis by Evolutionary Optimization of Coulombic Interactions
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Thermostabilisation of the Serotonin Transporter in a Cocaine-Bound Conformation
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A crystal clear solution for determining G-protein-coupled receptor structures
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Origins of the High Stability of an in vitro-selected Cold-shock Protein
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[34] Structural basis of thermostability in hyperthermophilic proteins, or “There's more than one way to skin a cat”
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Cold-shock response and cold-shock proteins
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Hot-Spot Residues to be Mutated Common in G Protein-Coupled Receptors of Class A: Identification of Thermostabilizing Mutations Followed by Determination of Three-Dimensional Structures for Two Example Receptors
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Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme
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Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima
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Structural and Dynamic Features of Cold-Shock Proteins of Listeria monocytogenes, a Psychrophilic Bacterium
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Two exposed amino acid residues confer thermostability on a cold shock protein.
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Saturation editing of genomic regions by multiplex homology-directed repair
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Local fitness landscape of the green fluorescent protein
inferredcites →https://doi.org/10.1038/nmeth.1492openalex-snapshot
High-resolution mapping of protein sequence-function relationships
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Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
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Learning the pattern of epistasis linking genotype and phenotype in a protein
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Multiplex assessment of protein variant abundance by massively parallel sequencing
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A primer on deep learning in genomics
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Responses of crop yield growth to global temperature and socioeconomic changes
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Structural basis for channelling mechanism of a fatty acid β‐oxidation multienzyme complex
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Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC
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CspB and CspL, thermostable cold‐shock proteins from Thermotoga maritima
inferredcites →https://doi.org/10.1073/pnas.0711253105openalex-snapshot
Conformational thermostabilization of the β1-adrenergic receptor in a detergent-resistant form
inferredcites →https://doi.org/10.1073/pnas.0803103105openalex-snapshot
Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity
inferredcites →https://doi.org/10.1073/pnas.0906510106openalex-snapshot
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins
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Increased body temperature accelerates aggregation ofthe Leu-68-->Gln mutant cystatin C, the amyloid-forming protein in hereditarycystatin C amyloid angiopathy.
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Tolerance of Arc repressor to multiple-alanine substitutions
inferredcites →https://doi.org/10.1074/jbc.m111496200openalex-snapshot
The Nucleic Acid Melting Activity of Escherichia coliCspE Is Critical for Transcription Antitermination and Cold Acclimation of Cells
inferredcites →https://doi.org/10.1074/jbc.m208118200openalex-snapshot
Three Amino Acids in Escherichia coli CspE Surface-exposed Aromatic Patch Are Critical for Nucleic Acid Melting Activity Leading to Transcription Antitermination and Cold Acclimation of Cells
inferredcites →https://doi.org/10.1093/bioinformatics/17.3.282openalex-snapshot
Clustering of highly homologous sequences to reduce the size of large protein databases
inferredcites →https://doi.org/10.1093/bioinformatics/btn166openalex-snapshot
Predicting protein thermostability changes from sequence upon multiple mutations
inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot
Biopython: freely available Python tools for computational molecular biology and bioinformatics
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Deep learning improves antimicrobial peptide recognition
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Predicting the optimal growth temperatures of prokaryotes using only genome derived features
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Low Temperature Adaptation Is Not the Opposite Process of High Temperature Adaptation in Terms of Changes in Amino Acid Composition
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Phenotypic severity of homozygous GCK mutations causing neonatal or childhood-onset diabetes is primarily mediated through effects on protein stability
inferredcites →https://doi.org/10.1093/nar/gkn072openalex-snapshot
PROMALS3D: a tool for multiple protein sequence and structure alignments
inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot
The Pfam protein families database: towards a more sustainable future
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BacDive – The Bacterial Diversity Metadatabase in 2016
inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gky1048openalex-snapshot
BRENDA in 2019: a European ELIXIR core data resource
inferredcites →https://doi.org/10.1093/oxfordjournals.jbchem.a124234openalex-snapshot
The Backbone Structure of the Major Cold-Shock Protein CS7.4 of Escherichia coli in Solution Includes Extensive β-Sheet Structure1
inferredcites →https://doi.org/10.1093/plankt/fbv009openalex-snapshot
Patterns of thermal limits of phytoplankton
inferredcites →https://doi.org/10.1093/protein/gzn001openalex-snapshot
Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity
inferredcites →https://doi.org/10.1109/icgtspicc.2016.7955308openalex-snapshot
Evolutionary algorithms: A critical review and its future prospects
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1110/ps.8.2.394openalex-snapshot
Cloning, overexpression, purification, and physicochemical characterization of a cold shock protein homolog from the hyperthermophilic bacterium Thermotoga maritima
inferredcites →https://doi.org/10.1110/ps.9.2.387openalex-snapshot
Contribution of proton linkage to the thermodynamic stability of the major cold‐shock protein of Escherichia coli CspA
inferredcites →https://doi.org/10.1126/science.aah3717openalex-snapshot
Evolutionary drivers of thermoadaptation in enzyme catalysis
inferredcites →https://doi.org/10.1128/jb.184.15.4246-4258.2002openalex-snapshot
pH-Dependent Expression of Periplasmic Proteins and Amino Acid Catabolism in Escherichia coli
inferredcites →https://doi.org/10.1186/s12866-018-1320-7openalex-snapshot
Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures
inferredcites →https://doi.org/10.1186/s13059-019-1845-6openalex-snapshot
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect
inferredcites →https://doi.org/10.1371/journal.pone.0063091openalex-snapshot
Marine Phytoplankton Temperature versus Growth Responses from Polar to Tropical Waters – Outcome of a Scientific Community-Wide Study
inferredcites →https://doi.org/10.2134/agronj2010.0303openalex-snapshot
Climate Impacts on Agriculture: Implications for Crop Production
inferredcites →https://doi.org/10.3389/fmicb.2016.01151openalex-snapshot
Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41467-022-35237-xopenalex-snapshot
Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
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