Search results
- 1.0463502 - ÚOCHB 2017 RIV US eng J - Journal Article
Jakubec, Dávid - Laskowski, R. A. - Vondrášek, Jiří
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
PLoS ONE. Roč. 11, č. 7 (2016), č. článku e0158704. ISSN 1932-6203. E-ISSN 1932-6203
R&D Projects: GA MŠMT(CZ) LH11020
Institutional support: RVO:61388963
Keywords : molecular electrostatic potentials * side-chain interactions * amino acid interactions
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 2.806, year: 2016
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158704
Permanent Link: http://hdl.handle.net/11104/0262680 - 2.0458534 - ÚOCHB 2017 RIV US eng J - Journal Article
Towse, C. L. - Vymětal, Jiří - Vondrášek, Jiří - Daggett, V.
Insights into Unfolded Proteins from the Intrinsic phi/psi Propensities of the AAXAA Host-Guest Series.
Biophysical Journal. Roč. 110, č. 2 (2016), s. 348-361. ISSN 0006-3495. E-ISSN 1542-0086
R&D Projects: GA MŠMT(CZ) LH11020
Institutional support: RVO:61388963
Keywords : polyproline-II helix * beta-sheet protein * random-coil behavior
Subject RIV: BO - Biophysics
Impact factor: 3.656, year: 2016
Permanent Link: http://hdl.handle.net/11104/0258790 - 3.0444348 - ÚOCHB 2016 RIV US eng J - Journal Article
Jakubec, Dávid - Hostaš, Jiří - Laskowski, R. A. - Hobza, Pavel - Vondrášek, Jiří
Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.
Journal of Chemical Theory and Computation. Roč. 11, č. 4 (2015), s. 1939-1948. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) LH11020
Institutional support: RVO:61388963
Keywords : DNA interactions * hydrogen bonds * recognition
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 5.301, year: 2015
Permanent Link: http://hdl.handle.net/11104/0247002 - 4.0438291 - ÚOCHB 2015 RIV GB eng J - Journal Article
Vymětal, Jiří - Bathula, S. R. - Černý, Jiří - Chaloupková, R. - Žídek, L. - Sklenář, V. - Vondrášek, Jiří
Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.
Protein Engineering Design and Selection. Roč. 27, č. 12 (2014), s. 463-472. ISSN 1741-0126. E-ISSN 1741-0134
R&D Projects: GA MŠMT(CZ) LH11020; GA ČR GA203/08/0114
Grant - others:GA MŠk(CZ) LO1214; GA MŠk(CZ) LM2010005; GA MŠk(CZ) ED1.1.00/02.0068
Program: ED
Institutional support: RVO:61388963 ; RVO:86652036
Keywords : protein folding * protein-structure prediction * molecular dynamics * NMR methods * CD spectroscopy
Subject RIV: CE - Biochemistry
Impact factor: 2.537, year: 2014
Permanent Link: http://hdl.handle.net/11104/0241840 - 5.0432453 - ÚOCHB 2015 RIV US eng J - Journal Article
Vymětal, Jiří - Vondrášek, Jiří
Parametrization of 2,2,2-Trifluoroethanol Based on the Generalized Amber Force Field Provides Realistic Agreement between Experimental and Calculated Properties of Pure Liquid as Well as Water-Mixed Solutions.
Journal of Physical Chemistry B. Roč. 118, č. 35 (2014), s. 10390-10404. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT(CZ) LH11020
Grant - others:GA MŠk(CZ) LM2010005
Institutional support: RVO:61388963
Keywords : molecular dynamics simulations * alpha-helical structure * der Waals interactions
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.302, year: 2014
Permanent Link: http://hdl.handle.net/11104/0236872 - 6.0429452 - ÚOCHB 2015 RIV GB eng J - Journal Article
Galgonek, Jakub - Vondrášek, Jiří
On InChI and evaluating the quality of cross-reference links.
Journal of Cheminformatics. Roč. 6, Apr 17 (2014), 15/1-15/15. ISSN 1758-2946. E-ISSN 1758-2946
R&D Projects: GA MŠMT(CZ) LH11020
Institutional support: RVO:61388963
Keywords : databases * system * file
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 4.547, year: 2014
http://www.jcheminf.com/content/6/1/15
Permanent Link: http://hdl.handle.net/11104/0234604 - 7.0396329 - ÚOCHB 2014 RIV GB eng J - Journal Article
Kysilka, Jiří - Vondrášek, Jiří
A systematic method for analysing the protein hydration structure of T4 lysozyme.
Journal of Molecular Recognition. Roč. 26, č. 10 (2013), s. 479-487. ISSN 0952-3499. E-ISSN 1099-1352
R&D Projects: GA ČR GAP208/10/0725; GA MŠMT(CZ) LH11020
Grant - others:GA ČR(CZ) GAP302/10/0427
Institutional support: RVO:61388963
Keywords : protein hydration structure * water * X-ray crystallography * cluster algorithm * interaction enthalpy
Subject RIV: CE - Biochemistry
Impact factor: 2.337, year: 2013
Permanent Link: http://hdl.handle.net/11104/0224147 - 8.0392241 - ÚOCHB 2014 RIV US eng J - Journal Article
Vymětal, Jiří - Vondrášek, Jiří
Critical Assessment of Current Force Fields. Short Peptide Test Case.
Journal of Chemical Theory and Computation. Roč. 9, č. 1 (2013), s. 441-451. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) LH11020
Grant - others:GA MŠk(CZ) LM2010005
Institutional support: RVO:61388963
Keywords : Helix-coil transition * protein-folding simulations * amino-acids * side-chain * alanine dipeptide
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 5.310, year: 2013
Permanent Link: http://hdl.handle.net/11104/0221161 - 9.0385763 - ÚOCHB 2013 RIV GB eng J - Journal Article
Kysilka, Jiří - Vondrášek, Jiří
Towards a better understanding of the specificity of protein-protein interaction.
Journal of Molecular Recognition. Roč. 25, č. 11 (2012), s. 604-615. ISSN 0952-3499. E-ISSN 1099-1352
R&D Projects: GA ČR GAP208/10/0725; GA ČR GAP302/10/0427; GA MŠMT(CZ) LH11020
Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50520701
Keywords : protein-protein interaction * molecular recognition * x-ray structure analysis * empirical potentials * side chain-side chain interaction * interaction energy * bioinformatics
Subject RIV: CE - Biochemistry
Impact factor: 3.006, year: 2012
Permanent Link: http://hdl.handle.net/11104/0156114 - 10.0384278 - ÚOCHB 2013 RIV US eng J - Journal Article
Fačkovec, Boris - Vondrášek, Jiří
Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications.
Journal of Physical Chemistry B. Roč. 116, č. 42 (2012), s. 12651-12660. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR GAP208/10/0725; GA MŠMT(CZ) LH11020
Institutional support: RVO:61388963
Keywords : egg-white lysozyme * force-field * 3-dimensional structure * thermophilic proteins * thermal-stability * mutant
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.607, year: 2012
Permanent Link: http://hdl.handle.net/11104/0007248