WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F86652036%3A_____%2F17%3A00480545" target="_blank" >RIV/86652036:_____/17:00480545 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1039/c7cp00187h" target="_blank" >http://dx.doi.org/10.1039/c7cp00187h</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1039/c7cp00187h" target="_blank" >10.1039/c7cp00187h</a>

Result language

angličtina

Original language name

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

Original language description

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Physical Chemistry Chemical Physics

ISSN

1463-9076

e-ISSN

—

Volume of the periodical

19

Issue of the periodical within the volume

26

Country of publishing house

GB - UNITED KINGDOM

Number of pages

8

Pages from-to

17094-17102

UT code for WoS article

000405422900016

EID of the result in the Scopus database

2-s2.0-85024485920