Research graph
References from How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
1961 · External reference
Unresolved reference
1994 · External reference
Unresolved reference
1986 · External reference
Protein Dynamics from NMR
10.1038/78963 · 2000 · External reference
10.1016/s0959-440x(96)80027-3
10.1016/s0959-440x(96)80027-3 · External reference
10.1126/science.1124964
10.1126/science.1124964 · External reference
10.1016/j.sbi.2006.01.006
10.1016/j.sbi.2006.01.006 · External reference
10.1016/j.sbi.2017.02.003
10.1016/j.sbi.2017.02.003 · External reference
10.1016/j.bbapap.2010.01.017
10.1016/j.bbapap.2010.01.017 · External reference
10.1042/bst20160172
10.1042/bst20160172 · External reference
10.1016/j.sbi.2018.09.007
10.1016/j.sbi.2018.09.007 · External reference
10.1007/978-3-319-20164-1
10.1007/978-3-319-20164-1 · 2015 · External reference
10.1016/j.csbj.2019.06.009
10.1016/j.csbj.2019.06.009 · External reference
10.1021/cr400688u
10.1021/cr400688u · External reference
Protien Crystallography for Aspiring Crystallographers
2013 · External reference
10.1002/pro.3248
10.1002/pro.3248 · External reference
10.1007/s10858-019-00280-2
10.1007/s10858-019-00280-2 · External reference
10.1093/bioinformatics/btl589
10.1093/bioinformatics/btl589 · External reference
10.1093/nar/gkw438
10.1093/nar/gkw438 · External reference
Molecular Dynamics Simulations: Advances and Applications
2015 · External reference
10.1016/j.drudis.2016.07.001
10.1016/j.drudis.2016.07.001 · External reference
10.1016/j.str.2010.04.016
10.1016/j.str.2010.04.016 · External reference
10.1038/nsb0902-646
10.1038/nsb0902-646 · External reference
Molecular Dynamics Simulation of Hen Egg white Lysozyme: A Test of the GROMOS96 Force Field against Nuclear Magnetic Resonance Data
10.1002/(sici)1097-0134(20000701)40:1<145::aid-prot160>3.0.co;2-y · 2000 · External reference
Motional Averaging of Proton Nuclear Overhauser Effects in Proteins. Predictions from a Molecular Dynamics Simulation of Lysozyme
10.1021/ja00319a004 · 1984 · External reference
Synergistic use of NMR and MD Simulations to Study the Structural Heterogeneity of Proteins
10.1002/wcms.1093 · 2012 · External reference
Membrane Proteins: Molecular Dynamics Simulations
10.1016/j.sbi.2008.02.003 · 2008 · External reference
10.1016/j.sbi.2017.10.008
10.1016/j.sbi.2017.10.008 · External reference
New Developments in Force Fields for Biomolecular Simulations
10.1016/j.sbi.2018.02.002 · 2018 · External reference
Validation of Molecular Dynamics Simulations of Biomolecules using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field
10.1021/ct7000045 · 2007 · External reference
10.1016/j.bpj.2010.04.062
10.1016/j.bpj.2010.04.062 · External reference
10.1023/a:1008365802830
10.1023/a:1008365802830 · External reference
10.1016/j.abb.2017.05.002
10.1016/j.abb.2017.05.002 · External reference
10.1371/journal.pcbi.1000168
10.1371/journal.pcbi.1000168 · External reference
Unresolved reference
2006 · External reference
10.1093/oso/9780198506348.001.0001
10.1093/oso/9780198506348.001.0001 · 2001 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
10.1038/78956
10.1038/78956 · External reference
Unresolved reference
External reference
Dead-Time Free Measurement of Dipole-Dipole Interactions Between Electron Spins
10.1016/j.jmr.2011.08.035 · 2011 · External reference
Recent Developments in Solution Nuclear Magnetic Resonance (NMR) -based Molecular Biology Timescales Detectable by NMR
10.1007/s00109-017-1560-2 · 2018 · External reference
10.1021/acs.jcim.8b00928
10.1021/acs.jcim.8b00928 · External reference
Combining MD Simulations and NMR Spectroscopy for Molecular Insight and Methodological Synergy: The Integrated MD-NMR Method
10.1039/9781782622758-00592 · 2015 · External reference
Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4
10.1021/ct400654r · 2013 · External reference
Novel Dimerization Fold of RAP30/RAP74 in Human TFIIF at 1.7 Å Resolution
2000 · External reference
10.1016/j.jmb.2018.04.008
10.1016/j.jmb.2018.04.008 · External reference
Drugs for “Protein Clouds”: Targeting Intrinsically Disordered Transcription Factors
10.1016/j.coph.2010.09.005 · 2010 · External reference
10.1016/j.sbi.2009.03.004
10.1016/j.sbi.2009.03.004 · External reference
10.1021/ct501178z
10.1021/ct501178z · External reference
Computer Simulations of Intrinsically Disordered Proteins
10.1146/annurev-physchem-052516-050843 · 2017 · External reference
Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation
10.1002/wcms.1167 · 2014 · External reference
10.1016/j.sbi.2018.09.008
10.1016/j.sbi.2018.09.008 · External reference
10.1016/s0959-440x(02)00289-0
10.1016/s0959-440x(02)00289-0 · External reference
10.1002/prot.340230111
10.1002/prot.340230111 · External reference
10.1021/ct500181v
10.1021/ct500181v · External reference
10.1016/j.sbi.2012.11.002
10.1016/j.sbi.2012.11.002 · External reference
10.1371/journal.pcbi.1003406
10.1371/journal.pcbi.1003406 · External reference
10.7554/elife.56518
10.7554/elife.56518 · External reference
Using the maximum entropy principle to combine simulations and solution experiments
10.3390/computation6010015 · 2018 · External reference
10.1021/acs.jpclett.0c02242
10.1021/acs.jpclett.0c02242 · External reference
10.1016/j.sbi.2007.01.009
10.1016/j.sbi.2007.01.009 · External reference
10.1093/nar/gkz291
10.1093/nar/gkz291 · External reference
Elucidating Transient Macromolecular Interactions using Paramagnetic Relaxation Enhancement
10.1016/j.sbi.2007.08.013 · 2007 · External reference
10.1002/cbic.201900453
10.1002/cbic.201900453 · External reference
10.1021/cr900033p
10.1021/cr900033p · External reference
10.1016/j.str.2011.02.002
10.1016/j.str.2011.02.002 · External reference
Presentation of Membrane-Anchored Glycosphingolipids Determined from Molecular Dynamics Simulations and NMR Paramagnetic Relaxation Rate Enhancement
10.1021/ja907518x · 2010 · External reference
10.1073/pnas.1111420108
10.1073/pnas.1111420108 · External reference
10.1007/s10858-011-9545-x
10.1007/s10858-011-9545-x · External reference
10.1021/cr030413t
10.1021/cr030413t · External reference
10.1016/s0959-440x(03)00036-8
10.1016/s0959-440x(03)00036-8 · External reference
10.1016/j.pnmrs.2010.12.003
10.1016/j.pnmrs.2010.12.003 · External reference
10.1021/ja00381a009
10.1021/ja00381a009 · External reference
10.1021/jacs.8b09107
10.1021/jacs.8b09107 · External reference
Understanding the Nature of Nuclear Magnetic Resonance Relaxation by Means of Fast-Field-Cycling Relaxometry and Molecular Dynamics Simulations - The Validity of Relaxation Models
10.1021/acs.jpclett.0c00087 · 2020 · External reference
10.1021/acs.biochem.7b00679
10.1021/acs.biochem.7b00679 · External reference
The Mechanism of Discrimination between Cognate and Non-Specific DNA by Dimeric b/HLH/LZ Transcription Factors
10.1016/j.jmb.2006.10.044 · 2007 · External reference
The MYC Transcription Factor Network: Balancing Metabolism
2018 · External reference
10.1016/j.str.2019.07.006
10.1016/j.str.2019.07.006 · External reference
Fragment-Based NMR Study of the Conformational Dynamics in the bHLH Transcription Factor Ascl1
10.1016/j.bpj.2017.02.025 · 2017 · External reference
Myc phosphorylation in its basic helix?loop?helix region destabilizes transient-helical structures, disrupting Max and DNA binding
10.1074/jbc.ra118.002709 · 2018 · External reference
10.1021/acs.chemrev.8b00513
10.1021/acs.chemrev.8b00513 · External reference
10.1016/j.cbpa.2019.08.007
10.1016/j.cbpa.2019.08.007 · External reference
10.1016/j.bbrc.2020.08.004
10.1016/j.bbrc.2020.08.004 · External reference
10.1073/pnas.1520483112
10.1073/pnas.1520483112 · External reference
10.1073/pnas.1318115111
10.1073/pnas.1318115111 · External reference
10.1021/jacs.9b08287
10.1021/jacs.9b08287 · External reference
10.1021/jacs.6b08416
10.1021/jacs.6b08416 · External reference
Intermolecular Paramagnetic Relaxation Enhancement (PRE) Studies of Transient Complexes in Intrinsically Disordered Proteins
10.1007/978-1-4939-2978-8_3 · 2016 · External reference
10.1038/s41586-020-2843-2
10.1038/s41586-020-2843-2 · External reference
Complete Coupled Binding-Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling
10.1021/acs.biochem.8b00441 · 2018 · External reference
10.1016/j.jmb.2018.02.015
10.1016/j.jmb.2018.02.015 · External reference
10.1002/cbic.202000348
10.1002/cbic.202000348 · External reference
10.1021/acs.biochem.8b00195
10.1021/acs.biochem.8b00195 · External reference
Model of the Interaction between the NF-κB Inhibitory Protein p100 and the E3 Ubiquitin Ligase β-TrCP based on NMR and Docking Experiments
10.1021/acs.jcim.5b00409 · 2017 · External reference
Side Chain to Main Chain Hydrogen Bonds Stabilize a Polyglutamine Helix in a Transcription Tactor
2019 · External reference
Dynamic Studies on Intrinsically Disordered Regions of Two Paralogous Transcription Factors Reveal Rigid Segments with Important Biological Functions
10.1016/j.jmb.2019.02.021 · 2019 · External reference
Structural and Dynamics Studies of Pax5 Reveal Asymmetry in Stability and DNA Binding by the Paired Domain
10.1016/j.jmb.2016.04.004 · 2016 · External reference
10.1021/acs.biochem.0c00737
10.1021/acs.biochem.0c00737 · External reference
10.1039/d0cp03473h
10.1039/d0cp03473h · External reference
Markov State Models and NMR Uncover an Overlooked Allosteric Loop in p53
10.1039/d0sc05053a · 2021 · External reference
10.1002/ijch.201900091
10.1002/ijch.201900091 · External reference
Site-Directed Spin Label Electron Paramagnetic Resonance Spectroscopy as a Probe of Conformational Dynamics in the Fe (III) “ Locked-Off ” State of the CO-Sensing Transcription Factor CooA
10.1002/pro.3449 · 2018 · External reference
10.1002/jcc.26032
10.1002/jcc.26032 · External reference
Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron-Electron Resonance Spectroscopy
10.1021/jp3110369 · 2014 · External reference
10.1093/nar/gkaa133
10.1093/nar/gkaa133 · External reference
“Hidden Side” of Spin Labeled Oligo Nucleotides: Molecular Dynamics Study Focusing on the EPR-Silent Components of Base Pairing
2020 · External reference
10.1039/c7cp04997h
10.1039/c7cp04997h · External reference
10.1016/j.jsb.2010.10.013
10.1016/j.jsb.2010.10.013 · External reference
10.1002/pro.3269
10.1002/pro.3269 · External reference
DEER-PREdict: Software for Efficient Calculation of Spin-Labeling EPR and NMR Data from Conformational Ensembles
2020 · External reference
10.1016/s0969-2126(97)00207-4
10.1016/s0969-2126(97)00207-4 · External reference
10.1002/1439-7641(20021115)3:11<927::aid-cphc927>3.0.co;2-q
10.1002/1439-7641(20021115)3:11<927::aid-cphc927>3.0.co;2-q · External reference
10.1021/acs.jpclett.6b00885
10.1021/acs.jpclett.6b00885 · External reference
10.1007/978-1-0716-0270-6_15
10.1007/978-1-0716-0270-6_15 · External reference
10.1021/ja069124n
10.1021/ja069124n · External reference
Information Theory and Statistical Mechanics
1957 · External reference
10.1073/pnas.96.2.332
10.1073/pnas.96.2.332 · External reference
10.1007/s10858-021-00358-w
10.1007/s10858-021-00358-w · External reference
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ḉ spin label
10.1093/nar/gkz1096 · 2020 · External reference
Integrated Computational Approach to the Electron Paramagnetic Resonance Characterization of Rigid 310-Helical Peptides with TOAC Nitroxide Spin Labels
10.1021/acs.jpcb.7b01050 · 2017 · External reference