Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase

(2016) Abraham López et al.   JOURNAL OF MASS SPECTROMETRY

Unravelling biological macromolecules with cryo-electron microscopy

(2016) Rafael Fernandez-Leiro et al.   NATURE

Automated structure modeling of large protein assemblies using crosslinks as distance restraints

(2016) Mathias Ferber et al.   NATURE METHODS

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

(2015) T. Xu et al.   Journal of Proteomics

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

(2015) Adam Belsom et al.   MOLECULAR & CELLULAR PROTEOMICS

Architecture of the RNA polymerase II–Mediator core initiation complex

(2015) C. Plaschka et al.   NATURE

Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering

(2015) Vincenzo Venditti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios

(2014) Chao Liu et al.   ANALYTICAL CHEMISTRY

Subtle Dynamics of holo Glutamine Binding Protein Revealed with a Rigid Paramagnetic Probe

(2014) Zhu Liu et al.   BIOCHEMISTRY

Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

(2014) Jan P. Erzberger et al.   CELL

14N15N DXMSMS Match program for the automated analysis of LC/ESI-MS/MS crosslinking data from experiments using 15N metabolically labeled proteins

(2014) Evgeniy V. Petrotchenko et al.   Journal of Proteomics

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

(2014) Yi Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

A mass spectrometry–based hybrid method for structural modeling of protein complexes

(2014) Argyris Politis et al.   NATURE METHODS

Analysis of Nidogen-1/Laminin γ1 Interaction by Cross-Linking, Mass Spectrometry, and Computational Modeling Reveals Multiple Binding Modes

(2014) Philip Lössl et al.   PLoS One

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances

(2014) Eric D. Merkley et al.   PROTEIN SCIENCE

ThreaDom: extracting protein domain boundary information from multiple threading alignments

(2013) Zhidong Xue et al.   BIOINFORMATICS

Cross-Link Guided Molecular Modeling with ROSETTA

(2013) Abdullah Kahraman et al.   PLoS One

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

(2013) A. Sekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

(2012) Thomas Walzthoeni et al.   NATURE METHODS

Identification of cross-linked peptides from complex samples

(2012) Bing Yang et al.   NATURE METHODS

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage

(2012) Stefan Jennebach et al.   NUCLEIC ACIDS RESEARCH

Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling

(2012) N. Kalisman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

(2012) K. Lasker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures

(2012) Guillermo A. Bermejo et al.   PROTEIN SCIENCE

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

Detection of a Protein Conformational Equilibrium by Electrospray Ionisation-Ion Mobility-Mass Spectrometry

(2011) Matthew Jenner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Xwalk: computing and visualizing distances in cross-linking experiments

(2011) Abdullah Kahraman et al.   BIOINFORMATICS

Transient, Sparsely Populated Compact States of Apo and Calcium-Loaded Calmodulin Probed by Paramagnetic Relaxation Enhancement: Interplay of Conformational Selection and Induced Fit

(2011) Nicholas J. Anthis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

(2011) Guillaume Bouvignies et al.   NATURE

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes

(2010) Juri Rappsilber   JOURNAL OF STRUCTURAL BIOLOGY

Accurate Solution Structures of Proteins from X-ray Data and a Minimal Set of NMR Data: Calmodulin−Peptide Complexes As Examples

(2009) Ivano Bertini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Probability-based shotgun cross-linking sites analysis

(2009) Young Jin Lee   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology