Cargando…

Protein–protein HADDocking using exclusively pseudocontact shifts

In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based...

Descripción completa

Detalles Bibliográficos
Autores principales:	Schmitz, Christophe, Bonvin, Alexandre M. J. J.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Springer Netherlands 2011
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133697/ https://www.ncbi.nlm.nih.gov/pubmed/21626213 http://dx.doi.org/10.1007/s10858-011-9514-4

Ejemplares similares

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
por: Honorato, Rodrigo V., et al.
Publicado: (2019)

Integral membrane protein structure determination using pseudocontact shifts
por: Crick, Duncan J., et al.
Publicado: (2015)

NMR pseudocontact shifts in a symmetric protein homotrimer
por: Müntener, Thomas, et al.
Publicado: (2020)

Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems
por: Kurkcuoglu, Zeynep, et al.
Publicado: (2019)

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance
por: van Dijk, Marc, et al.
Publicado: (2010)

An automated iterative approach for protein structure refinement using pseudocontact shifts
por: Cucuzza, Stefano, et al.
Publicado: (2021)

Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility
por: van Dijk, Marc, et al.
Publicado: (2006)

Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4
por: Charitou, Vicky, et al.
Publicado: (2022)

Methyl group assignment using pseudocontact shifts with PARAssign
por: Lescanne, Mathilde, et al.
Publicado: (2017)

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking
por: Spiliotopoulos, Dimitrios, et al.
Publicado: (2016)

HADDOCK(2P2I): A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors
por: Kastritis, Panagiotis L., et al.
Publicado: (2014)

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
por: de Vries, Sjoerd J., et al.
Publicado: (2011)

MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry
por: Hennig, Janosch, et al.
Publicado: (2012)

Methyl group reorientation under ligand binding probed by pseudocontact shifts
por: Lescanne, Mathilde, et al.
Publicado: (2018)

Localising nuclear spins by pseudocontact shifts from a single tagging site
por: Orton, Henry W., et al.
Publicado: (2022)

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK
por: Roel-Touris, Jorge, et al.
Publicado: (2019)

Building Macromolecular Assemblies by Information-driven Docking: INTRODUCING THE HADDOCK MULTIBODY DOCKING SERVER
por: Karaca, Ezgi, et al.
Publicado: (2010)

A dysprosium single molecule magnet outperforming current pseudocontact shift agents
por: Santana, Francielli S., et al.
Publicado: (2022)

Model-free extraction of spin label position distributions from pseudocontact shift data
por: Suturina, Elizaveta A., et al.
Publicado: (2017)

Localization of ligands within human carbonic anhydrase II using (19)F pseudocontact shift analysis
por: Zimmermann, Kaspar, et al.
Publicado: (2019)

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts
por: Pan, Yun-Zu, et al.
Publicado: (2016)

Solution Structure of a Lanthanide‐binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints
por: Andrałojć, Witold, et al.
Publicado: (2022)

Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
por: Vangone, A., et al.
Publicado: (2016)

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
por: Kurkcuoglu, Zeynep, et al.
Publicado: (2017)

Solution of a Puzzle: High-Level Quantum-Chemical Treatment of Pseudocontact Chemical Shifts Confirms Classic Semiempirical Theory
por: Lang, Lucas, et al.
Publicado: (2020)

Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites
por: Orton, Henry W., et al.
Publicado: (2022)

Assignment of Ala, Ile, Leu(proS), Met, and Val(proS) methyl groups of the protruding domain of murine norovirus capsid protein VP1 using methyl–methyl NOEs, site directed mutagenesis, and pseudocontact shifts
por: Maass, Thorben, et al.
Publicado: (2022)

Atlantic Haddock (Melanogrammus aeglefinus) Larvae Have a Magnetic Compass that Guides Their Orientation
por: Cresci, Alessandro, et al.
Publicado: (2019)

Underwater sound from vessel traffic reduces the effective communication range in Atlantic cod and haddock
por: Stanley, Jenni A., et al.
Publicado: (2017)

Thermal biology and swimming performance of Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus)
por: Norin, Tommy, et al.
Publicado: (2019)

Crude oil exposures reveal roles for intracellular calcium cycling in haddock craniofacial and cardiac development
por: Sørhus, Elin, et al.
Publicado: (2016)

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
por: Tørresen, Ole K., et al.
Publicado: (2018)

Unexpected Interaction with Dispersed Crude Oil Droplets Drives Severe Toxicity in Atlantic Haddock Embryos
por: Sørhus, Elin, et al.
Publicado: (2015)

Oil droplet fouling and differential toxicokinetics of polycyclic aromatic hydrocarbons in embryos of Atlantic haddock and cod
por: Sørensen, Lisbet, et al.
Publicado: (2017)

Tracking oocyte development and the timing of skipped spawning for north‐east Arctic haddock ( Melanogrammus aeglefinus )
por: Tronbøl, Frida, et al.
Publicado: (2022)

Contacts-based prediction of binding affinity in protein–protein complexes
por: Vangone, Anna, et al.
Publicado: (2015)

Sensory and Physicochemical Quality Characteristics of Haddock Fish Cake Enriched with Atlantic Mackerel Quality of Fish Cakes
por: Cropotova, Janna, et al.
Publicado: (2021)

Spatio-temporal distribution and acoustic characterization of haddock (Melanogrammus aeglefinus, Gadidae) calls in the Arctic fjord Kongsfjorden (Svalbard Islands)
por: Buscaino, G., et al.
Publicado: (2020)

A protein–DNA docking benchmark
por: van Dijk, Marc, et al.
Publicado: (2008)

Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
por: Jandova, Zuzana, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_vb840skji1mevuqm2n09nerggp