Refinement of protein structures in explicit solvent

By J. Linge, Mark A. Williams, Chris A. E. M. Spronk, Alexandre M. J. J. Bonvin, M. Nilges. Proteins: Structure, Function, and Bioinformatics, 2003

627 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f2117f109e37cc0bc6e440903481fbc74f7464ca

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Yuanpeng Janet Huang
4. Gaetano T. Montelione
5. A. V. van Dijk
6. V. Hsu
7. Rolf Boelens
8. Andriy Kryshtafovych

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Gaetano T. Montelione
4. Yuanpeng Janet Huang
5. A. V. van Dijk
6. V. Hsu
7. Rolf Boelens
8. M. Nilges

Citations in the corpus

• A topology‐constrained distance network algorithm for protein structure determination from NOESY data (2005, positive): “Refinement by restrained molecular dynamics in explicit solvent 68 can also improve the sterochemical quality of the final 3D structures generated by AutoStructure/ XPLOR.”
• Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility (2006, methodology): “OPLSX non-bonded parameters from the parallhdg5.3.pro parameter file ( 36 ) were used for the protein.”
• A protein–DNA docking benchmark (2008, methodology): “Atom and residue names were matched to the topallhdg5.3.pro ( 11 ) and dna-rna_allatom.top topology files (12) naming for direct use in HADDOCK (13).”
• Structural insights into the recruitment of SMRT by the corepressor SHARP under phosphorylative regulation. (2013, methodology): “Finally, structures were refined using a water refinement protocol (Linge et al., 2003).”
• ARIA: automated NOE assignment and NMR structure calculation (2003, methodology): “We have shown that few solvent molecules in a thin layer around the protein are sufficient to account for most important effects of water, notably polar and nonpolar interactions on the protein surface (Linge et al., 2003).”