Research graph
References from Conformational dynamics of fuzzy interfaces in disordered protein complexes: mapping key residues and binding modes beyond NMR models. Local targets link to admitted publications; unresolved targets remain external evidence.
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
Pressure control using stochastic cell rescaling
10.1063/5.0020514 · 2020 · External reference
The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex
10.1016/j.molcel.2011.11.008 · 2011 · External reference
Canonical sampling through velocity rescaling
10.1063/1.2408420 · 2007 · External reference
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles
10.1093/nar/gkac365 · 2022 · External reference
RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures
10.1093/nar/gkae337 · 2024 · External reference
Particle mesh ewald: an n⋅log(N) method for ewald sums in large systems
10.1063/1.464397 · 1993 · External reference
Peptide folding: when simulation meets experiment
10.1002/(sici)1521-3773(19990115)38:1/2<236::aid-anie236>3.0.co;2-m · 1999 · External reference
Structure of the Tfb1/p53 complex: insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53
10.1016/j.molcel.2006.05.007 · 2006 · External reference
Intrinsically disordered protein
10.1016/s1093-3263(00)00138-8 · 2001 · External reference
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins
10.1093/nar/gkad947 · 2024 · External reference
UCSF ChimeraX: meeting modern challenges in visualization and analysis
10.1002/pro.3235 · 2018 · External reference
Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins
10.1093/bioinformatics/btae627 · 2024 · External reference
Best practices for quantification of uncertainty and sampling quality in molecular simulations [article v1.0]
10.33011/livecoms.1.1.5067 · 2018 · External reference
The rules of disorder or why disorder rules
10.1016/j.pbiomolbio.2009.03.001 · 2009 · External reference
FuzDB: a new phase in understanding fuzzy interactions
10.1093/nar/gkab1060 · 2022 · External reference
Characterising intrinsically disordered proteins using NMR
10.1039/9781839165702-00383 · 2022 · External reference
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
10.1038/nmeth.4067 · 2017 · External reference
VMD: visual molecular dynamics
10.1016/0263-7855(96)00018-5 · 1996 · External reference
Differential transactivation by the p53 transcription factor is highly dependent on p53 level and promoter target sequence
10.1128/mcb.22.24.8612-8625.2002 · 2002 · External reference
Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-κB and transcription regulatory factors
10.1093/nar/gkx146 · 2017 · External reference
Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein
10.1021/bi1012996 · 2010 · External reference
NMR spin relaxation enables the selection of realistic intrinsically disordered protein ensembles from molecular dynamics simulations
10.1038/s42004-026-02155-8 · 2026 · External reference
Fuzziness enables context dependence of protein interactions
10.1002/1873-3468.12762 · External reference
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies
10.1093/nar/gkw1019 · External reference
Unresolved reference
2025 · External reference
Developing a molecular dynamics force field for both folded and disordered protein states
10.1073/pnas.1800690115 · 2018 · External reference
HMGB1-facilitated p53 DNA binding occurs via HMG-Box/p53 transactivation domain interaction, regulated by the acidic tail
10.1016/j.str.2012.09.004 · 2012 · External reference
Unresolved reference
2024 · External reference
Convergent views on disordered protein dynamics from NMR and computational approaches
10.1016/j.bpj.2022.09.016 · 2022 · External reference
Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP
10.1016/s1097-2765(03)00115-1 · 2003 · External reference
Fuzzy complexes: specific binding without complete folding
10.1016/j.febslet.2015.07.022 · 2015 · External reference
Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation
10.1074/jbc.m507059200 · 2005 · External reference
10.1201/9781420078930
10.1201/9781420078930 · 2009 · External reference
Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions
10.1016/j.tibs.2007.10.003 · 2008 · External reference
The protein ensemble database
10.1007/978-3-319-20164-1_11 · 2015 · External reference
Classification of intrinsically disordered regions and proteins
10.1021/cr400525m · 2014 · External reference
GROMACS: fast, flexible, and free
10.1002/jcc.20291 · 2005 · External reference
Improving the quality of co-evolution intermolecular contact prediction with DisVis
10.1002/prot.26514 · 2023 · External reference
The intrinsic affinity between E2 and the cys domain of E1 in ubiquitin-like modifications
10.1016/j.molcel.2007.05.023 · 2007 · External reference
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
10.1016/j.jmb.2004.02.002 · 2004 · External reference
Ensemble determination by NMR data deconvolution
10.1038/s41570-023-00494-x · 2023 · External reference
Linking folding and binding
10.1016/j.sbi.2008.12.003 · 2009 · External reference
Intrinsically disordered proteins in cellular signalling and regulation
10.1038/nrm3920 · 2015 · External reference
The structure and dynamics of higher-order assemblies: amyloids, signalosomes, and granules
10.1016/j.cell.2016.05.004 · 2016 · External reference
Computational prediction of protein interfaces: a review of data driven methods
10.1016/j.febslet.2015.10.003 · 2015 · External reference
Protein-protein recognition: exploring the energy funnels near the binding sites
10.1002/(sici)1097-0134(19990201)34:2<255::aid-prot10>3.0.co;2-o · 1999 · External reference
Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3’-splice site recognition
10.1093/nar/gks1097 · 2013 · External reference
