Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F15%3A10315393" target="_blank" >RIV/00216208:11310/15:10315393 - isvavai.cz</a>
Alternative codes found
RIV/61388963:_____/15:00449320 RIV/61989592:15310/15:33157045
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.5b00398" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.5b00398</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.5b00398" target="_blank" >10.1021/acs.jctc.5b00398</a>

Result language
angličtina
Original language name
Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems
Original language description
Representative pairs of amino acid side chains and nucleic acid bases extracted from available high-quality structures of protein DNA complexes were analyzed using a range of computational methods. CCSD(T)/CBS interaction energies were calculated for thechosen 272 pairs. These reference interaction energies were used to test the MP2.5/CBS, MP2.X/ CBS, MP2-F12, DFT-D3, PM6, and Amber force field methods. Method MP2.5 provided excellent agreement with reference data (root-mean-square error (RMSE) of 0.11kcal/mol), which is more than 1 order of magnitude faster than the CCSD(T) method. When MP2-F12 and MP2.5 were combined, the results were within reasonable accuracy (0.20 kcal/mol), with a computational savings of almost 2 orders of magnitude: Therefore, this method is a promising tool for accurate calculations of interaction energies in protein DNA motifs of up to similar to 100 atoms, for which CCSD(T)/CBS benchmark calculations are not feasible. B3-LYP-D3 calculated with def2-TZVPP a
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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