skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: DRoP: Automated detection of conserved solvent‐binding sites on proteins

Authors:
 [1];  [2]; ORCiD logo [2];  [3];  [3];  [3]; ORCiD logo [1]
  1. Department of Chemistry and Chemical BiologyNortheastern University Boston Massachusetts, Department of Molecular and Structural BiochemistryNorth Carolina State University Raleigh North Carolina
  2. Department of Chemistry and Chemical BiologyNortheastern University Boston Massachusetts
  3. Department of Molecular and Structural BiochemistryNorth Carolina State University Raleigh North Carolina
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1544453
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Proteins
Additional Journal Information:
Journal Name: Proteins Journal Volume: 88 Journal Issue: 1; Journal ID: ISSN 0887-3585
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Kearney, Bradley M., Schwabe, Michael, Marcus, Kendra C., Roberts, Daniel M., Dechene, Michelle, Swartz, Paul, and Mattos, Carla. DRoP: Automated detection of conserved solvent‐binding sites on proteins. United States: N. p., 2019. Web. doi:10.1002/prot.25781.
Kearney, Bradley M., Schwabe, Michael, Marcus, Kendra C., Roberts, Daniel M., Dechene, Michelle, Swartz, Paul, & Mattos, Carla. DRoP: Automated detection of conserved solvent‐binding sites on proteins. United States. doi:10.1002/prot.25781.
Kearney, Bradley M., Schwabe, Michael, Marcus, Kendra C., Roberts, Daniel M., Dechene, Michelle, Swartz, Paul, and Mattos, Carla. Tue . "DRoP: Automated detection of conserved solvent‐binding sites on proteins". United States. doi:10.1002/prot.25781.
@article{osti_1544453,
title = {DRoP: Automated detection of conserved solvent‐binding sites on proteins},
author = {Kearney, Bradley M. and Schwabe, Michael and Marcus, Kendra C. and Roberts, Daniel M. and Dechene, Michelle and Swartz, Paul and Mattos, Carla},
abstractNote = {},
doi = {10.1002/prot.25781},
journal = {Proteins},
number = 1,
volume = 88,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/prot.25781

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Minimizing frustration by folding in an aqueous environment
journal, January 2008


MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein−Protein Interface
journal, January 2009

  • Wong, Sergio; Amaro, Rommie E.; McCammon, J. Andrew
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 2
  • DOI: 10.1021/ct8003707

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
journal, September 1998

  • Shindyalov, I. N.; Bourne, P. E.
  • Protein Engineering Design and Selection, Vol. 11, Issue 9
  • DOI: 10.1093/protein/11.9.739

Ribonuclease A
journal, May 1998


Analysis of solvent structure in proteins using neutron D2OH2O solvent maps: Pattern of primary and secondary hydration of trypsin
journal, March 1992

  • Kossiakoff, Anthony A.; Sintchak, Michael D.; Shpungin, Joseph
  • Proteins: Structure, Function, and Genetics, Vol. 12, Issue 3
  • DOI: 10.1002/prot.340120303

Exploring structurally conserved solvent sites in protein families
journal, May 2006

  • Bottoms, Christopher A.; White, Tommi A.; Tanner, John J.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 2
  • DOI: 10.1002/prot.21014

Ribonuclease structure and catalysis: crystal structure of sulfate-free native ribonuclease A at 1.5- .ANG. resolution
journal, December 1987

  • Campbell, Robert L.; Petsko, Gregory A.
  • Biochemistry, Vol. 26, Issue 26
  • DOI: 10.1021/bi00400a013

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection
journal, September 2016

  • Maciag, Joseph J.; Mackenzie, Sarah H.; Tucker, Matthew B.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 41
  • DOI: 10.1073/pnas.1603549113

Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description
journal, March 2007

  • Teyra, Joan; Pisabarro, M. T.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 67, Issue 4
  • DOI: 10.1002/prot.21394

Multiple Solvent Crystal Structures: Probing Binding Sites, Plasticity and Hydration
journal, April 2006

  • Mattos, Carla; Bellamacina, Cornelia R.; Peisach, Ezra
  • Journal of Molecular Biology, Vol. 357, Issue 5
  • DOI: 10.1016/j.jmb.2006.01.039

The structures of rnase a complexed with 3′-CMP and d(CpA): Active site conformation and conserved water molecules
journal, December 1994

  • Zegers, Ingrid; Maes, Dominique; Dao-Thi, Minh-Hoa
  • Protein Science, Vol. 3, Issue 12
  • DOI: 10.1002/pro.5560031217

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Analysis of the binding surfaces of proteins
journal, July 1999


Locating the catalytic water molecule in serine proteases
journal, July 1993


Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol
journal, December 1999


DRoP: A Water Analysis Program Identifies Ras-GTP-Specific Pathway of Communication between Membrane-Interacting Regions and the Active Site
journal, February 2014

  • Kearney, Bradley M.; Johnson, Christian W.; Roberts, Daniel M.
  • Journal of Molecular Biology, Vol. 426, Issue 3
  • DOI: 10.1016/j.jmb.2013.10.036

Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme
journal, July 1994


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Structure of phosphate-free ribonuclease A refined at 1.26 .ANG.
journal, April 1988

  • Wlodawer, Alexander; Svensson, L. Anders; Sjoelin, Lennart
  • Biochemistry, Vol. 27, Issue 8
  • DOI: 10.1021/bi00408a010

Protein–water interactions in a dynamic world
journal, April 2002


Buried water in homologous serine proteases
journal, December 1992


Fragment-based lead discovery: leads by design
journal, July 2005


Analysis of Binding Site Hot Spots on the Surface of Ras GTPase
journal, November 2011

  • Buhrman, Greg; O′Connor, Casey; Zerbe, Brandon
  • Journal of Molecular Biology, Vol. 413, Issue 4
  • DOI: 10.1016/j.jmb.2011.09.011

Comparison of two independently refined models of ribonuclease-A
journal, August 1986

  • Wlodawer, A.; Borkakoti, N.; Moss, D. S.
  • Acta Crystallographica Section B Structural Science, Vol. 42, Issue 4
  • DOI: 10.1107/S0108768186098063

Multiple solvent crystal structures of ribonuclease A: An assessment of the method
journal, September 2009

  • Dechene, Michelle; Wink, Glenna; Smith, Mychal
  • Proteins: Structure, Function, and Bioinformatics, Vol. 76, Issue 4
  • DOI: 10.1002/prot.22393

The Protein Data Bank
journal, January 2000


Structural basis of an engineered dual-specific antibody: conformational diversity leads to a hypervariable loop metal-binding site
journal, August 2014

  • Fanning, Sean W.; Walter, Richard; Horn, James R.
  • Protein Engineering, Design and Selection, Vol. 27, Issue 10
  • DOI: 10.1093/protein/gzu033

Exploring Expression Data: Identification and Analysis of Coexpressed Genes
journal, November 1999