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References from AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein. Local targets link to admitted publications; unresolved targets remain external evidence.
Why are "natively unfolded" proteins unstructured under physiologic conditions?
10.1002/1097-0134(20001115)41:3<415::aid-prot130>3.0.co;2-7 · 2000 · External reference
Natively unfolded proteins: a point where biology waits for physics
10.1110/ps.4210102 · 2002 · External reference
A decade and a half of protein intrinsic disorder: biology still waits for physics
10.1002/pro.2261 · 2013 · External reference
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
10.1006/jmbi.1999.3110 · 1999 · External reference
Natively unfolded proteins
10.1016/j.sbi.2005.01.002 · 2005 · External reference
What’s in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered
10.4161/idp.24157 · 2013 · External reference
Intrinsically disordered proteins: Chronology of a discovery
10.1016/j.bpc.2021.106694 · 2021 · External reference
Biomolecular condensates: organizers of cellular biochemistry
10.1038/nrm.2017.7 · 2017 · External reference
Intrinsically disordered proteins: emerging interaction specialists
10.1016/j.sbi.2015.08.009 · 2015 · External reference
Intrinsically disordered proteins in cellular signalling and regulation
10.1038/nrm3920 · 2015 · External reference
The evolutionary origins of cell type diversification and the role of intrinsically disordered proteins
10.1093/jxb/erx493 · 2018 · External reference
Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins
10.1074/jbc.r115.685859 · 2016 · External reference
Fuzzy protein theory for disordered proteins
10.1042/bst20200239 · 2020 · External reference
Paradoxes and wonders of intrinsic disorder: Complexity of simplicity
10.1080/21690707.2015.1135015 · 2016 · External reference
Resources for computational prediction of intrinsic disorder in proteins
10.1016/j.ymeth.2022.03.018 · 2022 · External reference
Principles that govern the folding of protein chains
10.1126/science.181.4096.223 · 1973 · External reference
High-accuracy protein structure prediction in CASP14
10.1002/prot.26171 · 2021 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Protein structure predictions to atomic accuracy with AlphaFold
10.1038/s41592-021-01362-6 · 2022 · External reference
Applying and improving AlphaFold at CASP14. Proteins: Structure, Function, and
2021 · External reference
Critical assessment of protein intrinsic disorder prediction
10.1038/s41592-021-01117-3 · 2021 · External reference
A community effort to bring structure to disorder
10.1038/s41592-021-01123-5 · 2021 · External reference
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
10.1093/nar/gkab1082 · 2022 · External reference
AlphaFold2: A Role for Disordered Protein/Region Prediction?
10.3390/ijms23094591 · 2022 · External reference
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
10.1093/nar/gkab1061 · 2022 · External reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · 2021 · External reference
AlphaFold heralds a data-driven revolution in biology and medicine
10.1038/s41591-021-01533-0 · 2021 · External reference
"Protein" no longer means what it used to
10.1016/j.crstbi.2021.06.002 · 2021 · External reference
RCSB Protein Data Bank: Enabling biomedical research and drug discovery
10.1002/pro.3730 · 2020 · External reference
AI revolutions in biology: The joys and perils of AlphaFold
10.15252/embr.202154046 · 2021 · External reference
Cutting Edge Structural Protein from the Jaws of Nereis virens
10.1021/bm800200a · 2008 · External reference
Ion Effect and Metal-Coordinated Cross-Linking for Multiscale Design of Nereis Jaw Inspired Mechanomutable Materials
10.1021/acsnano.6b07878 · 2017 · External reference
Programmable Mechanical Properties from a Worm Jaw-Derived Biopolymer through Hierarchical Ion Exposure
10.1021/acsami.8b10107 · 2018 · External reference
Protein complex prediction with AlphaFold-Multimer
2021 · External reference
Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review
10.1016/j.csbj.2019.06.009 · 2019 · External reference
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
10.1038/s42003-021-01759-1 · 2021 · External reference
Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polfuluoroalkyl substance) biodegradation
2023 · External reference
TM-align: a protein structure alignment algorithm based on the TM-score
10.1093/nar/gki524 · 2005 · External reference
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
10.1093/nar/gkp318 · 2009 · External reference
APE: Analyses of Phylogenetics and Evolution in R language
10.1093/bioinformatics/btg412 · 2004 · External reference
Scalable molecular dynamics with NAMD
10.1002/jcc.20289 · 2005 · External reference
Scalable molecular dynamics on CPU and GPU architectures with NAMD
10.1063/5.0014475 · 2020 · External reference
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
10.1038/nmeth.4067 · 2017 · External reference
A modified TIP3P water potential for simulation with Ewald summation
10.1063/1.1808117 · 2004 · External reference
VMD: visual molecular dynamics
10.1016/0263-7855(96)00018-5 · 1996 · External reference
Measurement of histidine pKa values and tautomer populations in invisible protein states
10.1073/pnas.1400577111 · 2014 · External reference
The igraph software package for complex network research
2006 · External reference
The Bio3D packages for structural bioinformatics
10.1002/pro.3923 · 2021 · External reference
Knowledge‐based protein secondary structure assignment
10.1002/prot.340230412 · 1995 · External reference
Single-sequence protein structure prediction using a language model and deep learning
10.1038/s41587-022-01432-w · 2022 · External reference
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding
10.1093/nar/gky384 · 2018 · External reference
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation
10.1093/nar/gkab408 · 2021 · External reference
Optimizing long intrinsic disorder predictors with protein evolutionary information
10.1142/s0219720005000886 · 2005 · External reference
Length-dependent prediction of protein intrinsic disorder
10.1186/1471-2105-7-208 · 2006 · External reference
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids
10.1016/j.bbapap.2010.01.011 · 2010 · External reference
Molecular Dynamics Investigation into pH Dependent Metal Binding of the Intrinsically Disordered Worm Jaw Protein, Nvjp-1
10.1021/acs.jpcb.2c02807 · 2022 · External reference
AlphaFold2 models indicate that protein sequence determines both structure and dynamics
10.1038/s41598-022-14382-9 · 2022 · External reference
Constructing ensembles for intrinsically disordered proteins
10.1016/j.sbi.2011.04.001 · 2011 · External reference
Accurate prediction of protein structures and interactions using a three-track neural network
10.1126/science.abj8754 · 2021 · External reference
A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon’s Information Theory
2019 · External reference
Protein flexibility, not disorder, is intrinsic to molecular recognition
10.3410/b5-2 · 2013 · External reference
Predicting multiple conformations via sequence clustering and AlphaFold2
10.1038/s41586-023-06832-9 · 2024 · External reference
