Post-translational modifications of proteins can have high impact on their structure, function, half-life, and many more. Considering the prediction and design of typical post-translational modifications such as N-linked or O-linked glycosylation during protein design is now possible through our integration of machine learning models in the Rosetta software suite. For N-linked glycosylation, we added structural features to the machine learning model to improve likelihood of glycan presence. Post-translational modifications can now actively be included or removed while designing the proteins sequence. Ertelt et al 2024
Image Credit: Moritz Ertelt
Education Articles
Twelve quick tips for deploying a Beacon
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011817
Ten simple rules for pushing boundaries of inclusion at academic events
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011797
Ten simple rules to leverage large language models for getting grants
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011863
Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices
PLOS Computational Biology: published March 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011936
Perspectives
For long-term sustainable software in bioinformatics
PLOS Computational Biology: published March 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011920
Ethical frameworks should be applied to computational modelling of infectious disease interventions
PLOS Computational Biology: published March 21, 2024 | https://doi.org/10.1371/journal.pcbi.1011933
Research Articles
When do stereotypes undermine indirect reciprocity?
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011862
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011247
Computational models of compound nerve action potentials: Efficient filter-based methods to quantify effects of tissue conductivities, conduction distance, and nerve fiber parameters
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011833
How neuronal morphology impacts the synchronisation state of neuronal networks
PLOS Computational Biology: published March 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011874
Dimensionality of locomotor behaviors in developing C. elegans
PLOS Computational Biology: published March 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011906
Unsupervised learning of perceptual feature combinations
PLOS Computational Biology: published March 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011926
Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation
PLOS Computational Biology: published March 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011918
Tipping points emerge from weak mutualism in metacommunities
PLOS Computational Biology: published March 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011899
LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies
PLOS Computational Biology: published March 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011881
Bifurcations and bursting in the Epileptor
PLOS Computational Biology: published March 6, 2024 | https://doi.org/10.1371/journal.pcbi.1011903
Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data
PLOS Computational Biology: published March 6, 2024 | https://doi.org/10.1371/journal.pcbi.1011888
Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations
PLOS Computational Biology: published March 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011921
Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein
PLOS Computational Biology: published March 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011955
Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions
PLOS Computational Biology: published March 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011917
Using early detection data to estimate the date of emergence of an epidemic outbreak
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Cortical cell assemblies and their underlying connectivity: An in silico study
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Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers
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AI-Aristotle: A physics-informed framework for systems biology gray-box identification
PLOS Computational Biology: published March 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011916
It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs
PLOS Computational Biology: published March 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011901
End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging
PLOS Computational Biology: published March 13, 2024 | https://doi.org/10.1371/journal.pcbi.1011074
Bayesian inference is facilitated by modular neural networks with different time scales
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Computational prediction of protein interactions in single cells by proximity sequencing
PLOS Computational Biology: published March 14, 2024 | https://doi.org/10.1371/journal.pcbi.1011915
CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network
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An analytically tractable, age-structured model of the impact of vector control on mosquito-transmitted infections
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Mathematical models of Plasmodium vivax transmission: A scoping review
PLOS Computational Biology: published March 14, 2024 | https://doi.org/10.1371/journal.pcbi.1011931
Unlocking ensemble ecosystem modelling for large and complex networks
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Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment
PLOS Computational Biology: published March 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011846
Bayesian inference of relative fitness on high-throughput pooled competition assays
PLOS Computational Biology: published March 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011937
Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study
PLOS Computational Biology: published March 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011944
Ensemble dynamics and information flow deduction from whole-brain imaging data
PLOS Computational Biology: published March 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011848
Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations
PLOS Computational Biology: published March 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011905
Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn
PLOS Computational Biology: published March 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011942
The condition for dynamic stability in humans walking with feedback control
PLOS Computational Biology: published March 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011861
Learning environment-specific learning rates
PLOS Computational Biology: published March 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011978
Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response
PLOS Computational Biology: published March 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011967
Modelling and analysis of cAMP-induced mixed-mode oscillations in cortical neurons: Critical roles of HCN and M-type potassium channels
PLOS Computational Biology: published March 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011559
Enrichment on steps, not genes, improves inference of differentially expressed pathways
PLOS Computational Biology: published March 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011968
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration
PLOS Computational Biology: published March 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011814
A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment
PLOS Computational Biology: published March 27, 2024 | https://doi.org/10.1371/journal.pcbi.1011984
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’s biomorphs
PLOS Computational Biology: published March 27, 2024 | https://doi.org/10.1371/journal.pcbi.1011893
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects
PLOS Computational Biology: published March 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011943
The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model
PLOS Computational Biology: published March 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011956
Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1
PLOS Computational Biology: published March 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011518
Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
PLOS Computational Biology: published March 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012008
Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models
PLOS Computational Biology: published March 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011640
Parameter estimation in behavioral epidemic models with endogenous societal risk-response
PLOS Computational Biology: published March 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011992
Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts
PLOS Computational Biology: published March 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011950
Methods
A multiscale computational framework for the development of spines in molluscan shells
PLOS Computational Biology: published March 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011835
teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering
PLOS Computational Biology: published March 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011929
Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins
PLOS Computational Biology: published March 14, 2024 | https://doi.org/10.1371/journal.pcbi.1011939
A machine-learning method for biobank-scale genetic prediction of blood group antigens
PLOS Computational Biology: published March 21, 2024 | https://doi.org/10.1371/journal.pcbi.1011977
Self-replicating artificial neural networks give rise to universal evolutionary dynamics
PLOS Computational Biology: published March 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012004
Software
kCSD-python, reliable current source density estimation with quality control
PLOS Computational Biology: published March 14, 2024 | https://doi.org/10.1371/journal.pcbi.1011941