Literature DB >> 16859297

Toward an alternative hardness kernel matrix structure in the Electronegativity Equalization Method (EEM).

J Chaves1, J M Barroso, P Bultinck, R Carbó-Dorca.   

Abstract

This study presents an alternative of the Electronegativity Equalization Method (EEM), where the usual Coulomb kernel has been transformed into a smooth function. The new framework, as the classical EEM, permits fast calculations of atomic charges in a given molecule for a small computational cost. The original EEM procedure needs to previously calibrate the different implied atomic hardness and electronegativity, using a chosen set of molecules. In the new EEM algorithm half the number of parameters needs to be calibrated, since a relationship between electronegativities and hardnesses has been found.

Entities:  

Mesh:

Year:  2006        PMID: 16859297     DOI: 10.1021/ci050505e

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  6 in total

1.  Charge sensitivity analysis in force-field-atom resolution.

Authors:  Anna Stachowicz; Anna Styrcz; Jacek Korchowiec
Journal:  J Mol Model       Date:  2011-03-03       Impact factor: 1.810

2.  How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

Authors:  Stanislav Geidl; Radka Svobodová Vařeková; Veronika Bendová; Lukáš Petrusek; Crina-Maria Ionescu; Zdeněk Jurka; Ruben Abagyan; Jaroslav Koča
Journal:  J Chem Inf Model       Date:  2015-06-11       Impact factor: 4.956

3.  Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation.

Authors:  Crina-Maria Ionescu; Radka Svobodová Vařeková; Jochen H M Prehn; Heinrich J Huber; Jaroslav Koča
Journal:  PLoS Comput Biol       Date:  2012-06-14       Impact factor: 4.475

4.  Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges.

Authors:  Tomáš Raček; Ondřej Schindler; Dominik Toušek; Vladimír Horský; Karel Berka; Jaroslav Koča; Radka Svobodová
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

5.  Predicting p Ka values from EEM atomic charges.

Authors:  Radka Svobodová Vařeková; Stanislav Geidl; Crina-Maria Ionescu; Ondřej Skřehota; Tomáš Bouchal; David Sehnal; Ruben Abagyan; Jaroslav Koča
Journal:  J Cheminform       Date:  2013-04-10       Impact factor: 5.514

6.  AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

Authors:  Crina-Maria Ionescu; David Sehnal; Francesco L Falginella; Purbaj Pant; Lukáš Pravda; Tomáš Bouchal; Radka Svobodová Vařeková; Stanislav Geidl; Jaroslav Koča
Journal:  J Cheminform       Date:  2015-10-22       Impact factor: 5.514

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.