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Items: 11

1.

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges.

Raček T, Pazúriková J, Svobodová Vařeková R, Geidl S, Křenek A, Falginella FL, Horský V, Hejret V, Koča J.

J Cheminform. 2016 Oct 17;8:57. eCollection 2016.

2.

The Eighth Central European Conference "Chemistry towards Biology": Snapshot.

Perczel A, Atanasov AG, Sklenář V, Nováček J, Papoušková V, Kadeřávek P, Žídek L, Kozłowski H, Wątły J, Hecel A, Kołkowska P, Koča J, Svobodová-Vařeková R, Pravda L, Sehnal D, Horský V, Geidl S, Enriz RD, Matějka P, Jeništová A, Dendisová M, Kokaislová A, Weissig V, Olsen M, Coffey A, Ajuebor J, Keary R, Sanz-Gaitero M, van Raaij MJ, McAuliffe O, Waltenberger B, Mocan A, Šmejkal K, Heiss EH, Diederich M, Musioł R, Košmrlj J, Polański J, Jampílek J.

Molecules. 2016 Oct 17;21(10). pii: E1381.

3.

High-quality and universal empirical atomic charges for chemoinformatics applications.

Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J.

J Cheminform. 2015 Dec 2;7:59. doi: 10.1186/s13321-015-0107-1. eCollection 2015.

4.

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

Ionescu CM, Sehnal D, Falginella FL, Pant P, Pravda L, Bouchal T, Svobodová Vařeková R, Geidl S, Koča J.

J Cheminform. 2015 Oct 22;7:50. doi: 10.1186/s13321-015-0099-x. eCollection 2015.

5.

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

Geidl S, Svobodová Vařeková R, Bendová V, Petrusek L, Ionescu CM, Jurka Z, Abagyan R, Koča J.

J Chem Inf Model. 2015 Jun 22;55(6):1088-97. doi: 10.1021/ci500758w. Epub 2015 Jun 11.

6.

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

Sehnal D, Svobodová Vařeková R, Pravda L, Ionescu CM, Geidl S, Horský V, Jaiswal D, Wimmerová M, Koča J.

Nucleic Acids Res. 2015 Jan;43(Database issue):D369-75. doi: 10.1093/nar/gku1118. Epub 2014 Nov 11.

7.

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.

Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426. Epub 2014 May 21.

8.

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

Ionescu CM, Geidl S, Svobodová Vařeková R, Koča J.

J Chem Inf Model. 2013 Oct 28;53(10):2548-58. doi: 10.1021/ci400448n. Epub 2013 Sep 13.

PMID:
23968236
9.

Predicting p Ka values from EEM atomic charges.

Vařeková RS, Geidl S, Ionescu CM, Skřehota O, Bouchal T, Sehnal D, Abagyan R, Koča J.

J Cheminform. 2013 Apr 10;5(1):18. doi: 10.1186/1758-2946-5-18.

10.

SiteBinder: an improved approach for comparing multiple protein structural motifs.

Sehnal D, Vařeková RS, Huber HJ, Geidl S, Ionescu CM, Wimmerová M, Koča J.

J Chem Inf Model. 2012 Feb 27;52(2):343-59. doi: 10.1021/ci200444d. Epub 2012 Feb 8.

PMID:
22296449
11.

Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes.

Svobodová Vareková R, Geidl S, Ionescu CM, Skrehota O, Kudera M, Sehnal D, Bouchal T, Abagyan R, Huber HJ, Koca J.

J Chem Inf Model. 2011 Aug 22;51(8):1795-806. doi: 10.1021/ci200133w. Epub 2011 Aug 1.

PMID:
21761919

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