The DNA binding domain of protein p53 is found complexed with many other proteins and DNA in the Protein Data Bank (PDB). The outer wheel shows soft disordered (in orange) and interface (in blue) regions observed in alternative crystals of these complexes. In the center, we show that once mapped on the structure, the union of all soft disordered regions and the union of all the interface regions tend to involve the same amino acids in the protein.
Image Credit: Beatriz Seoane
Editorial
Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students
PLOS Computational Biology: published January 14, 2021 | https://doi.org/10.1371/journal.pcbi.1008539
Topic Page
Chemical graph generators
PLOS Computational Biology: published January 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008504
Research Articles
Improving probabilistic infectious disease forecasting through coherence
PLOS Computational Biology: published January 6, 2021 | https://doi.org/10.1371/journal.pcbi.1007623
Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains
PLOS Computational Biology: published January 25, 2021 | https://doi.org/10.1371/journal.pcbi.1007675
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions
PLOS Computational Biology: published January 25, 2021 | https://doi.org/10.1371/journal.pcbi.1007694
Structured environments foster competitor coexistence by manipulating interspecies interfaces
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1007762
Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1007814
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1007900
Persistent thermal input controls steering behavior in Caenorhabditis elegans
PLOS Computational Biology: published January 8, 2021 | https://doi.org/10.1371/journal.pcbi.1007916
Coordinating cell polarization and morphogenesis through mechanical feedback
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1007971
Physical constraints on early blastomere packings
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1007994
A multiscale model of complex endothelial cell dynamics in early angiogenesis
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008055
A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response
PLOS Computational Biology: published January 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008066
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008114
Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system
PLOS Computational Biology: published January 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008130
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008169
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008208
Friendly-rivalry solution to the iterated n-person public-goods game
PLOS Computational Biology: published January 21, 2021 | https://doi.org/10.1371/journal.pcbi.1008217
Causal network inference from gene transcriptional time-series response to glucocorticoids
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008223
Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008231
Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008284
Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008310
Related Articles
Active probing to highlight approaching transitions to ictal states in coupled neural mass models
PLOS Computational Biology: published January 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008377
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008400
Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex
PLOS Computational Biology: published January 21, 2021 | https://doi.org/10.1371/journal.pcbi.1008414
Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission
PLOS Computational Biology: published January 14, 2021 | https://doi.org/10.1371/journal.pcbi.1008417
Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008446
The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008470
Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2
PLOS Computational Biology: published January 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008474
Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008486
MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome
PLOS Computational Biology: published January 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008487
Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects
PLOS Computational Biology: published January 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008499
Related Articles
Predicting synchronous firing of large neural populations from sequential recordings
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008501
Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008517
Minimal biophysical model of combined antibiotic action
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008529
Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008532
Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008535
Sensor-based localization of epidemic sources on human mobility networks
PLOS Computational Biology: published January 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008545
The complexity of protein interactions unravelled from structural disorder
PLOS Computational Biology: published January 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008546
Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008547
CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008550
Related Articles
DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
PLOS Computational Biology: published January 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008551
Model based planners reflect on their model-free propensities
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008552
Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach
PLOS Computational Biology: published January 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008555
On the role of transcription in positioning nucleosomes
PLOS Computational Biology: published January 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008556
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast
PLOS Computational Biology: published January 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008560
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk
PLOS Computational Biology: published January 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008561
Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference
PLOS Computational Biology: published January 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008564
Online analysis of microendoscopic 1-photon calcium imaging data streams
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008565
The risks of using the chi-square periodogram to estimate the period of biological rhythms
PLOS Computational Biology: published January 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008567
Rosetta design with co-evolutionary information retains protein function
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008568
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
PLOS Computational Biology: published January 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008569
Reconciling kinetic and thermodynamic models of bacterial transcription
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008572
Coincident glutamatergic depolarizations enhance GABAA receptor-dependent Cl- influx in mature and suppress Cl- efflux in immature neurons
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008573
Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008584
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
PLOS Computational Biology: published January 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008585
Real-time resolution of short-read assembly graph using ONT long reads
PLOS Computational Biology: published January 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008586
Four different mechanisms for switching cell polarity
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008587
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008596
Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing
PLOS Computational Biology: published January 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008597
A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008598
Estimating and interpreting secondary attack risk: Binomial considered biased
PLOS Computational Biology: published January 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008601
Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008603
Post-lockdown abatement of COVID-19 by fast periodic switching
PLOS Computational Biology: published January 21, 2021 | https://doi.org/10.1371/journal.pcbi.1008604
Machine learning based CRISPR gRNA design for therapeutic exon skipping
PLOS Computational Biology: published January 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008605
PASA: Proteomic analysis of serum antibodies web server
PLOS Computational Biology: published January 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008607
Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008609
Aggregative cycles evolve as a solution to conflicts in social investment
PLOS Computational Biology: published January 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008617
Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies
PLOS Computational Biology: published January 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008619
Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008620
Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model
PLOS Computational Biology: published January 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008624
mbkmeans: Fast clustering for single cell data using mini-batch k-means
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008625
Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics
PLOS Computational Biology: published January 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008627
Sparse deep predictive coding captures contour integration capabilities of the early visual system
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008629
Modeling invasion patterns in the glioblastoma battlefield
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008632
Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008634
A reconstruction theory of relational schema induction
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008641
The impact of interactions on invasion and colonization resistance in microbial communities
PLOS Computational Biology: published January 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008643
Modeling multi-sensory feedback control of zebrafish in a flow
PLOS Computational Biology: published January 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008644
Related Articles
PEtab—Interoperable specification of parameter estimation problems in systems biology
PLOS Computational Biology: published January 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008646
ProMod3—A versatile homology modelling toolbox
PLOS Computational Biology: published January 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008667
A sensory integration account for time perception
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008668
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
PLOS Computational Biology: published January 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008678
Estimating the time-varying reproduction number of COVID-19 with a state-space method
PLOS Computational Biology: published January 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008679