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Title: Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison

Authors:
ORCiD logo; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1600777
Resource Type:
Journal Article
Journal Name:
Journal of Computer-Aided Molecular Design
Additional Journal Information:
Journal Volume: 33; Journal Issue: 3; Journal ID: ISSN 0920-654X
Publisher:
Springer
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Nittinger, Eva, Gibbons, Paul, Eigenbrot, Charles, Davies, Doug R., Maurer, Brigitte, Yu, Christine L., Kiefer, James R., Kuglstatter, Andreas, Murray, Jeremy, Ortwine, Daniel F., Tang, Yong, and Tsui, Vickie. Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison. United States: N. p., 2019. Web. doi:10.1007/s10822-019-00187-y.
Nittinger, Eva, Gibbons, Paul, Eigenbrot, Charles, Davies, Doug R., Maurer, Brigitte, Yu, Christine L., Kiefer, James R., Kuglstatter, Andreas, Murray, Jeremy, Ortwine, Daniel F., Tang, Yong, & Tsui, Vickie. Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison. United States. doi:10.1007/s10822-019-00187-y.
Nittinger, Eva, Gibbons, Paul, Eigenbrot, Charles, Davies, Doug R., Maurer, Brigitte, Yu, Christine L., Kiefer, James R., Kuglstatter, Andreas, Murray, Jeremy, Ortwine, Daniel F., Tang, Yong, and Tsui, Vickie. Tue . "Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison". United States. doi:10.1007/s10822-019-00187-y.
@article{osti_1600777,
title = {Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison},
author = {Nittinger, Eva and Gibbons, Paul and Eigenbrot, Charles and Davies, Doug R. and Maurer, Brigitte and Yu, Christine L. and Kiefer, James R. and Kuglstatter, Andreas and Murray, Jeremy and Ortwine, Daniel F. and Tang, Yong and Tsui, Vickie},
abstractNote = {},
doi = {10.1007/s10822-019-00187-y},
journal = {Journal of Computer-Aided Molecular Design},
issn = {0920-654X},
number = 3,
volume = 33,
place = {United States},
year = {2019},
month = {2}
}

Works referenced in this record:

Superstar: improved knowledge-based interaction fields for protein binding sites11Edited by R. Huber
journal, March 2001

  • Verdonk, Marcel L.; Cole, Jason C.; Watson, Paul
  • Journal of Molecular Biology, Vol. 307, Issue 3
  • DOI: 10.1006/jmbi.2001.4452

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations
journal, July 2015

  • Bietz, Stefan; Rarey, Matthias
  • Journal of Chemical Information and Modeling, Vol. 55, Issue 8
  • DOI: 10.1021/acs.jcim.5b00210

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites
journal, February 2008

  • Amadasi, Alessio; Surface, J. Andrew; Spyrakis, Francesca
  • Journal of Medicinal Chemistry, Vol. 51, Issue 4
  • DOI: 10.1021/jm701023h

Erratum: “Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril” [J. Chem. Phys. 137, 044101 (2012)]
journal, October 2012

  • Nguyen, Crystal N.; Young, Tom Kurtzman; Gilson, Michael K.
  • The Journal of Chemical Physics, Vol. 137, Issue 14
  • DOI: 10.1063/1.4751113

Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6
journal, July 2010

  • Chrencik, Jill E.; Patny, Akshay; Leung, Iris K.
  • Journal of Molecular Biology, Vol. 400, Issue 3
  • DOI: 10.1016/j.jmb.2010.05.020

AQUARIUS2: Knowledge-based modeling of solvent sites around proteins
journal, September 1993

  • Pitt, William R.; Murray-Rust, Judith; Goodfellow, Julia M.
  • Journal of Computational Chemistry, Vol. 14, Issue 9
  • DOI: 10.1002/jcc.540140902

Potent and selective Bruton’s tyrosine kinase inhibitors: Discovery of GDC-0834
journal, March 2015

  • Young, Wendy B.; Barbosa, James; Blomgren, Peter
  • Bioorganic & Medicinal Chemistry Letters, Vol. 25, Issue 6
  • DOI: 10.1016/j.bmcl.2015.01.032

A Role for Hydration in Interleukin-2 Inducible T Cell Kinase (Itk) Selectivity
journal, November 2011

  • Knegtel, Ronald M. A.; Robinson, Daniel D.
  • Molecular Informatics, Vol. 30, Issue 11-12
  • DOI: 10.1002/minf.201100086

Strategies to Calculate Water Binding Free Energies in Protein–Ligand Complexes
journal, May 2014

  • Bodnarchuk, Michael S.; Viner, Russell; Michel, Julien
  • Journal of Chemical Information and Modeling, Vol. 54, Issue 6
  • DOI: 10.1021/ci400674k

Battling Btk Mutants With Noncovalent Inhibitors That Overcome Cys481 and Thr474 Mutations
journal, August 2016


Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa
journal, April 2014

  • Nguyen, Crystal N.; Cruz, Anthony; Gilson, Michael K.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 7
  • DOI: 10.1021/ct401110x

Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid
journal, January 1975


Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures
journal, October 2017

  • Meyder, Agnes; Nittinger, Eva; Lange, Gudrun
  • Journal of Chemical Information and Modeling, Vol. 57, Issue 10
  • DOI: 10.1021/acs.jcim.7b00391

Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density
journal, March 2015

  • Nittinger, Eva; Schneider, Nadine; Lange, Gudrun
  • Journal of Chemical Information and Modeling, Vol. 55, Issue 4
  • DOI: 10.1021/ci500662d

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery
journal, May 2017

  • Spyrakis, Francesca; Ahmed, Mostafa H.; Bayden, Alexander S.
  • Journal of Medicinal Chemistry, Vol. 60, Issue 16
  • DOI: 10.1021/acs.jmedchem.7b00057

Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains
journal, May 2016


Prediction of the Water Content in Protein Binding Sites
journal, October 2009

  • Michel, Julien; Tirado-Rives, Julian; Jorgensen, William L.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 40
  • DOI: 10.1021/jp9047456

A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP):  Theory and Application
journal, January 2007

  • Baroni, Massimo; Cruciani, Gabriele; Sciabola, Simone
  • Journal of Chemical Information and Modeling, Vol. 47, Issue 2
  • DOI: 10.1021/ci600253e

Modelling of solvent positions around polar groups in proteins
journal, January 1991

  • Pitt, William R.; Goodfellow, Julia M.
  • "Protein Engineering, Design and Selection", Vol. 4, Issue 5
  • DOI: 10.1093/protein/4.5.531

Discovery of highly potent and selective Bruton’s tyrosine kinase inhibitors: Pyridazinone analogs with improved metabolic stability
journal, January 2016

  • Young, Wendy B.; Barbosa, James; Blomgren, Peter
  • Bioorganic & Medicinal Chemistry Letters, Vol. 26, Issue 2
  • DOI: 10.1016/j.bmcl.2015.11.076

Structure–activity relationship study of 2,4-diaminothiazoles as Cdk5/p25 kinase inhibitors
journal, April 2011

  • Laha, Joydev K.; Zhang, Xuemei; Qiao, Lixin
  • Bioorganic & Medicinal Chemistry Letters, Vol. 21, Issue 7
  • DOI: 10.1016/j.bmcl.2011.01.140

A Perspective on Water Site Prediction Methods for Structure Based Drug Design
journal, August 2017


The Importance of Being Exhaustive. Optimization of Bridging Structural Water Molecules and Water Networks in Models of Biological Systems
journal, January 2004

  • Kellogg, Glen E.; Chen, Deliang L.
  • Chemistry & Biodiversity, Vol. 1, Issue 1
  • DOI: 10.1002/cbdv.200490016

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding
journal, March 2008

  • Abel, Robert; Young, Tom; Farid, Ramy
  • Journal of the American Chemical Society, Vol. 130, Issue 9
  • DOI: 10.1021/ja0771033

SuperStar: A Knowledge-based Approach for Identifying Interaction Sites in Proteins
journal, June 1999

  • Verdonk, Marcel L.; Cole, Jason C.; Taylor, Robin
  • Journal of Molecular Biology, Vol. 289, Issue 4
  • DOI: 10.1006/jmbi.1999.2809

Classification of Water Molecules in Protein Binding Sites
journal, March 2007

  • Barillari, Caterina; Taylor, Justine; Viner, Russell
  • Journal of the American Chemical Society, Vol. 129, Issue 9
  • DOI: 10.1021/ja066980q

Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm
journal, January 1997

  • Raymer, Michael L.; Sanschagrin, Paul C.; Punch, William F.
  • Journal of Molecular Biology, Vol. 265, Issue 4
  • DOI: 10.1006/jmbi.1996.0746

Discovery of Potent and Selective Tricyclic Inhibitors of Bruton’s Tyrosine Kinase with Improved Druglike Properties
journal, May 2017


High-energy water sites determine peptide binding affinity and specificity of PDZ domains
journal, August 2009

  • Beuming, Thijs; Farid, Ramy; Sherman, Woody
  • Protein Science, Vol. 18, Issue 8
  • DOI: 10.1002/pro.177

Identification of a Benzoisoxazoloazepine Inhibitor (CPI-0610) of the Bromodomain and Extra-Terminal (BET) Family as a Candidate for Human Clinical Trials
journal, April 2015

  • Albrecht, Brian K.; Gehling, Victor S.; Hewitt, Michael C.
  • Journal of Medicinal Chemistry, Vol. 59, Issue 4
  • DOI: 10.1021/acs.jmedchem.5b01882

SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles
journal, December 2015

  • Bietz, Stefan; Rarey, Matthias
  • Journal of Chemical Information and Modeling, Vol. 56, Issue 1
  • DOI: 10.1021/acs.jcim.5b00588

Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory
journal, April 1998

  • Lazaridis, Themis
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp9723574

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP
journal, July 2015

  • Bayden, Alexander S.; Moustakas, Demetri T.; Joseph-McCarthy, Diane
  • Journal of Chemical Information and Modeling, Vol. 55, Issue 8
  • DOI: 10.1021/ci500746d

From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library
journal, November 2017


Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids
journal, April 1998

  • Lazaridis, Themis
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp972358w

New insights from structural biology into the druggability of G protein-coupled receptors
journal, May 2012

  • Mason, Jonathan S.; Bortolato, Andrea; Congreve, Miles
  • Trends in Pharmacological Sciences, Vol. 33, Issue 5
  • DOI: 10.1016/j.tips.2012.02.005

Discovery of GDC-0853: A Potent, Selective, and Noncovalent Bruton’s Tyrosine Kinase Inhibitor in Early Clinical Development
journal, February 2018


Specific Btk inhibition suppresses B cell– and myeloid cell–mediated arthritis
journal, November 2010

  • Di Paolo, Julie A.; Huang, Tao; Balazs, Mercedesz
  • Nature Chemical Biology, Vol. 7, Issue 1
  • DOI: 10.1038/nchembio.481

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics
journal, January 2018

  • Graham, Sarah E.; Smith, Richard D.; Carlson, Heather A.
  • Journal of Chemical Information and Modeling, Vol. 58, Issue 2
  • DOI: 10.1021/acs.jcim.7b00268

Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods
journal, February 2018

  • Bucher, Denis; Stouten, Pieter; Triballeau, Nicolas
  • Journal of Chemical Information and Modeling, Vol. 58, Issue 3
  • DOI: 10.1021/acs.jcim.7b00642

Water Network Perturbation in Ligand Binding: Adenosine A 2A Antagonists as a Case Study
journal, June 2013

  • Bortolato, Andrea; Tehan, Ben G.; Bodnarchuk, Michael S.
  • Journal of Chemical Information and Modeling, Vol. 53, Issue 7
  • DOI: 10.1021/ci4001458