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Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density
- Source :
- Journal of Chemical Information and Modeling. 55:771-783
- Publication Year :
- 2015
- Publisher :
- American Chemical Society (ACS), 2015.
-
Abstract
- Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.
- Subjects :
- Models, Molecular
Electron density
Protein Conformation
Hydrogen bond
Chemistry
General Chemical Engineering
Proteins
Water
Electrons
Hydrogen Bonding
General Chemistry
computer.file_format
Library and Information Sciences
Protein Data Bank
Acceptor
Computer Science Applications
Hydrophobic effect
Computational chemistry
Chemical physics
Molecule
Databases, Protein
Hydrophobic and Hydrophilic Interactions
computer
Binding affinities
Subjects
Details
- ISSN :
- 1549960X and 15499596
- Volume :
- 55
- Database :
- OpenAIRE
- Journal :
- Journal of Chemical Information and Modeling
- Accession number :
- edsair.doi.dedup.....646af5fb93db86a3ff80de760a29b055