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Type IV pilus structure and bacterial pathogenicity
Type IV pili are remarkably strong, flexible filaments with varied roles in bacterial pathogenicity. All Gram-negative bacterial surfaces have type IV pili, which are polymeric assemblies of the… Expand
Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions.
Type IV pili (T4P) are long, thin, flexible filaments on bacteria that undergo assembly-disassembly from inner membrane pilin subunits and exhibit astonishing multifunctionality. Neisseria… Expand
Computational protein–ligand docking and virtual drug screening with the AutoDock suite
- S. Forli, R. Huey, M. Pique, M. Sanner, D. Goodsell, A. Olson
- Medicine, Biology
- Nature Protocols
- 1 May 2016
Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study of… Expand
Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin.
Pilin assembly into type IV pili is required for virulence by bacterial pathogens that cause diseases such as cholera, pneumonia, gonorrhea, and meningitis. Crystal structures of soluble,… Expand
Protein docking using continuum electrostatics and geometric fit.
- J. G. Mandell, V. Roberts, +5 authors L. T. Ten Eyck
- Medicine, Chemistry
- Protein engineering
- 1 February 2001
The computer program DOT quickly finds low-energy docked structures for two proteins by performing a systematic search over six degrees of freedom. A novel feature of DOT is its energy function,… Expand
Definition of the interaction domain for cytochrome c on cytochrome c oxidase. III. Prediction of the docked complex by a complete, systematic search.
The electron transfer complex between bovine cytochrome c oxidase and horse cytochrome c has been predicted with the docking program DOT, which performs a complete, systematic search over all six… Expand
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute
- Jesus M. Castagnetto, Sean W. Hennessy, V. Roberts, E. Getzoff, J. Tainer, M. Pique
- Computer Science, Medicine
- Nucleic Acids Res.
The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific… Expand
Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry.
The bacterial pathogen Vibrio cholerae uses toxin-coregulated pili (TCP) to colonize the human intestine, causing the severe diarrheal disease cholera. TCP are long, thin, flexible homopolymers of… Expand
XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair*♦
- M. Hammel, Martial Rey, +10 authors J. Tainer
- Medicine, Biology
- The Journal of Biological Chemistry
- 20 July 2011
The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts… Expand
DOT2: Macromolecular docking with improved biophysical models
- V. Roberts, Elaine E. Thompson, M. Pique, M. S. Perez, L. F. Eyck
- Medicine, Computer Science
- J. Comput. Chem.
- 30 July 2013
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of… Expand