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1

Dispersion Interactions Govern the Strong Thermal Stability of a Protein

Jiří Vondrášek, Tomáš Kubař, Francis E. Jenney Jr., Michael W. W. Adams, Milan Kožíšek, Jiří Černý, Vladimír Sklenář, Pavel Hobza

Journal:

Chemistry - A European Journal

Year:

2007

Language:

english

File:

PDF, 404 KB

english, 2007

2

Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins

Lubomı́r Rulı́šek, Jiřı́ Vondrášek

Journal:

Journal of Inorganic Biochemistry

Year:

1998

Language:

english

File:

PDF, 132 KB

english, 1998

3

INHIBITORS OF HIV-1 PROTEASE: A Major Success of Structure-Assisted Drug Design1

Wlodawer, Alexander, Vondrasek, Jiri

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

1998

Language:

english

File:

PDF, 466 KB

english, 1998

4

Highly selective purification of three lipases from Geotrichum candidum 4013 and their characterization and biotechnological applications

Brabcová, Jana, Demianová, Zuzana, Vondrášek, Jiří, Jágr, Michal, Zarevúcka, Marie, Palomo, Jose M.

Journal:

Journal of Molecular Catalysis B: Enzymatic

Year:

2013

Language:

english

File:

PDF, 2.35 MB

english, 2013

5

Solid phase synthesis of glycopeptide dendrimers with Tn antigenic structure and their biological activities. Part I

Jan Ježek, Jiří Velek, Pavel Vepřek, Vlasta Velková, Tomáš Trnka, Jaroslav Pecka, Miroslav Ledvina, Jiří Vondrášek, Martin Písačka

Journal:

Journal of Peptide Science

Year:

1999

Language:

english

File:

PDF, 225 KB

english, 1999

6

Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin

Karel Berka, Pavel Hobza, Jiří Vondrášek

Journal:

Year:

2009

Language:

english

File:

PDF, 280 KB

english, 2009

7

The DF-LCCSD(T0) correction of the φ/ψ force field dihedral parameters significantly influences the free energy profile of the alanine dipeptide

Jiří Vymětal, Jiří Vondrášek

Journal:

Chemical Physics Letters

Year:

2011

Language:

english

File:

PDF, 1.06 MB

english, 2011

8

HIVdb: A Database of the Structures of Human Immunodeficiency Virus Protease

Jiri Vondrasek, Alexander Wlodawer

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 38 KB

english, 2002

9

Application of InChI to curate, index, and query 3-D structures

M.D. Prasanna, Jiri Vondrasek, Alexander Wlodawer, T.N. Bhat

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 239 KB

english, 2005

10

Chemical compound navigator: A web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds

M.D. Prasanna, Jiri Vondrasek, Alexander Wlodawer, H. Rodriguez, T. N. Bhat

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 544 KB

english, 2006

11

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

Lada Bendová-Biedermannová, Pavel Hobza, Jiří Vondrášek

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 856 KB

english, 2008

12

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G

Jawid N. Ahmad, Jingjing Li, Lada Biedermannová, Milan Kuchař, Hana Šípová, Alena Semerádtová, Jiří Černý, Hana Petroková, Pavel Mikulecký, Jiří Polínek, Ondřej Staněk, Jiří Vondrášek, Jiří Homola, Ja

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 2.06 MB

english, 2012

13

Magnesium and biological activity of oxytocin analogues modified on aromatic ring of amino acid in position 2

Jiřina Slaninová, Lenka Maletínská, Jiří Vondrášek, Zdenko Procházka

Journal:

Journal of Peptide Science

Year:

2001

Language:

english

File:

PDF, 181 KB

english, 2001

14

Sexual Attraction in the Silkworm Moth: Nature of Binding of Bombykol in Pheromone Binding Protein—An Ab Initio Study

Vojtěch Klusák, Zdeněk Havlas, Lubomı́r Rulı́šek, Jiřı́ Vondrášek, Aleš Svatoš

Journal:

Chemistry & Biology

Year:

2003

Language:

english

File:

PDF, 214 KB

english, 2003

15

Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein

Jiří Vymětal, Ivan Slabý, Axel Spahr, Jiří Vondrášek, S. Petter Lyngstadaas

Journal:

European Journal of Oral Sciences

Year:

2008

Language:

english

File:

PDF, 1.89 MB

english, 2008

16

Database of three-dimensional structures of HIV proteinases

Vondrasek, Jiri, van Buskirk, Christopher P., Wlodawer, Alexander

Journal:

Natural Structural Biology

Year:

1997

File:

PDF, 177 KB

1997

17

Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane

Biedermannova, Lada, E. Riley, Kevin, Berka, Karel, Hobza, Pavel, Vondrasek, Jiri

Journal:

Physical Chemistry Chemical Physics

Year:

2008

Language:

english

File:

PDF, 977 KB

english, 2008

18

Free-thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I)

Martin Horn, Miroslav Baudyš, Zdeněk Voburka, Ivan Kluh, Jiří Vondrášek, Michael Mareš

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 1.48 MB

english, 2002

19

Database of HIV proteinase structures

Jiri Vondrasek, Alexander Wlodawer

Journal:

Trends in Biochemical Sciences

Year:

1997

Language:

english

File:

PDF, 740 KB

english, 1997

20

Biophysical characterization of recombinant human ameloblastin

Tomáš Wald, Lucie Bednárová, Radim Osička, Petr Pachl, Miroslav Šulc, Stale Petter Lyngstadaas, Ivan Slaby, Jiří Vondrášek

Journal:

European Journal of Oral Sciences

Year:

2011

Language:

english

File:

PDF, 438 KB

english, 2011

21

Configurations of Diastereomeric Hydroxyethylene Isosteres Strongly Affect Biological Activities of a Series of Specific Inhibitors of Human-Immunodeficiency-Virus Proteinase

Jan Konvalinka, Jaroslav Litera, Jan Weber, Jiří Vondrášek, Martin Hradílek, Milan Souček, Iva Pichová, Pavel Majer, Petr Štrop, Juraj Sedlácek, Anke-Mareil Heuser, Hubert Kottler, Hans-Georg Kräussli

Journal:

Year:

1997

Language:

english

File:

PDF, 2.89 MB

english, 1997

22

Potency Comparison of Peptidomimetic Inhibitors against HIV-1 and HIV-2 Proteinases: Design of Equipotent Lead Compounds

Jan Weber, Pavel Majer, Jaroslav Litera, Jan Urban, Milan Souček, Jiřı&amp, #x0301, Vondrášek, Jan Konvalinka, Petr Novek, Juraj Sedláček, Petr Štrop, Hans-Georg Kräusslich, Iva Pichová

Journal:

Archives of Biochemistry and Biophysics

Year:

1997

Language:

english

File:

PDF, 600 KB

english, 1997

23

A Picomolar Inhibitor of Resistant Strains of Human Immunodeficiency Virus Protease Identified by a Combinatorial Approach

Markéta Rinnová, Martin Hradilek, Cyril Bařinka, Jan Weber, Milan Souček, Jiřı́ Vondrášek, Thomas Klimkait, Jan Konvalinka

Journal:

Archives of Biochemistry and Biophysics

Year:

2000

Language:

english

File:

PDF, 684 KB

english, 2000

24

A Modular Approach to HIV-1 Proteinase Inhibitor Design

Tat'ána Uhlı&amp, #x0301, ková, Jan Konvalinka, Iva Pichová, Milan Souček, Hans-Georg Kräusslich, Jiřı&amp, #x0301, Vondrášek

Journal:

Biochemical and Biophysical Research Communications

Year:

1996

Language:

english

File:

PDF, 82 KB

english, 1996

25

Thermodynamic Penalty Arising from Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor

Elizabeth Barratt, Agnieszka Bronowska, Jiří Vondrášek, Jiří Černý, Richard Bingham, Simon Phillips, Steve W. Homans

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 614 KB

english, 2006

26

Critical Assessment of Current Force Fields. Short Peptide Test Case

Vymětal, Jiří, Vondrášek, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.36 MB

english, 2013

27

Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding

Vymětal, Jiří, Vondrášek, Jiří

Journal:

Journal of Physical Chemistry A

Year:

2011

Language:

english

File:

PDF, 6.96 MB

english, 2011

28

Towards a better understanding of the specificity of protein-protein interaction

Kysilka, Jiří, Vondrášek, Jiří

Journal:

Journal of Molecular Recognition

Year:

2012

Language:

english

File:

PDF, 2.26 MB

english, 2012

29

Unexpectedly Strong Energy Stabilization Inside the Hydrophobic Core of Small Protein Rubredoxin Mediated by Aromatic Residues: Correlated Ab Initio Quantum Chemical Calculations

Vondrášek, Jiří, Bendová, Lada, Klusák, Vojtěch, Hobza, Pavel

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 169 KB

english, 2005

30

Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest

Riley, Kevin E., Vondrášek, Jiři, Hobza, Pavel

Journal:

Physical Chemistry Chemical Physics

Year:

2007

Language:

english

File:

PDF, 836 KB

english, 2007

31

Like-Charge Guanidinium Pairing from Molecular Dynamics and Ab Initio Calculations

Vazdar, Mario, Vymětal, Jiři, Heyda, Jan, Vondrášek, Jiři, Jungwirth, Pavel

Journal:

Journal of Physical Chemistry A

Year:

2011

Language:

english

File:

PDF, 3.12 MB

english, 2011

32

On InChI and evaluating the quality of cross-reference links

Galgonek, Jakub, Vondrášek, Jiří

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 287 KB

english, 2014

33

Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications

Fačkovec, Boris, Vondrášek, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.93 MB

english, 2012

34

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

Vymětal, Jiří, Vondrášek, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 2.20 MB

english, 2014

35

Cathepsin D Propeptide: Mechanism and Regulation of Its Interaction with the Catalytic Core †

Máša, Martin, Marešová, Lucie, Vondrášek, Jiří, Horn, Martin, Ježek, Jan, Mareš, Michael

Journal:

Year:

2006

Language:

english

File:

PDF, 373 KB

english, 2006

36

Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease

Heyda, Jan, Pokorná, Jana, Vrbka, Luboš, Vácha, Robert, Jagoda-Cwiklik, Barbara, Konvalinka, Jan, Jungwirth, Pavel, Vondrášek, Jiří

Journal:

Physical Chemistry Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.20 MB

english, 2009

37

Unexpectedly Strong Energy Stabilization Inside the Hydrophobic Core of Small Protein Rubredoxin Mediated by Aromatic Residues: Correlated Ab Initio Quantum Chemical Calculations [ J. Amer. Chem. Soc. 2005 , 127 , 2615−2617].

Vondrasek, Jiri, Bendova, Lada, Klusak, Vojtech, Hobza, Pavel

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 11 KB

english, 2005

38

Quasiplanarity of the Peptide Bond

Chalupský, Jakub, Vondrášek, Jiří, Špirko, Vladimír

Journal:

Journal of Physical Chemistry A

Year:

2008

Language:

english

File:

PDF, 137 KB

english, 2008

39

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

Yin, Shuangye, Biedermannova, Lada, Vondrasek, Jiri, Dokholyan, Nikolay V.

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 536 KB

english, 2008

40

Model of Peptide Bond−Aromatic Ring Interaction: Correlated Ab Initio Quantum Chemical Study

Bendová, Lada, Jurečka, Petr, Hobza, Pavel, Vondrášek, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 151 KB

english, 2007

41

Activation Route of the Schistosoma mansoni Cathepsin B1 Drug Target: Structural Map with a Glycosaminoglycan Switch

Jílková, Adéla, Horn, Martin, Řezáčová, Pavlína, Marešová, Lucie, Fajtová, Pavla, Brynda, Jiří, Vondrášek, Jiří, McKerrow, James H., Caffrey, Conor R., Mareš, Michael

Journal:

Year:

2014

Language:

english

File:

PDF, 3.34 MB

english, 2014

42

Effect of Enamel Matrix Derivative and of Proline-Rich Synthetic Peptides on the Differentiation of Human Mesenchymal Stem Cells Toward the Osteogenic Lineage

Ramis, Joana Maria, Rubert, Marina, Vondrasek, Jiri, Gayà, Antoni, Lyngstadaas, Staale Petter, Monjo, Marta

Journal:

Tissue Engineering Part A

Year:

2012

Language:

english

File:

PDF, 662 KB

english, 2012

43

An Empirical Potential Study of the Interaction of L—;Lysine—;L—;Alanine—;L—;Alanine Tripeptide with Four models of B—;DNA with different Compositions

Vondrásek, Jiří, Šponar, Jaroslav, Hobza, Pavel

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

1994

Language:

english

File:

PDF, 872 KB

english, 1994

44

Large-Scale Quantitative Assessment of Binding Preferences in Protein–Nucleic Acid Complexes

Jakubec, Dávid, Hostaš, Jiří, Laskowski, Roman A., Hobza, Pavel, Vondrášek, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.34 MB

english, 2015

45

Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors

Caffrey, Conor R., Placha, Lenka, Barinka, Cyril, Hradilek, Martin, Dostál, Jiří, Sajid, Mohammed, McKerrow, James H., Majer, Pavel, Konvalinka, Jan, Vondrášek, Jiří

Journal:

Biological Chemistry

Year:

2005

Language:

english

File:

PDF, 351 KB

english, 2005

46

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

Klusák, Vojtěch, Dobeš, Petr, Černý, Jiří, Vondrášek, Jiří

Journal:

Collection of Czechoslovak Chemical Communications

Year:

2011

Language:

english

File:

PDF, 591 KB

english, 2011

47

PIP2 and PIP3 interact with N-terminus region of TRPM4 channel

Bousova, Kristyna, Jirku, Michaela, Bumba, Ladislav, Bednarova, Lucie, Sulc, Miroslav, Franek, Miloslav, Vyklicky, Ladislav, Vondrasek, Jiri, Teisinger, Jan

Journal:

Biophysical Chemistry

Year:

2015

Language:

english

File:

PDF, 1.46 MB

english, 2015

48

Increasing Affinity of Interferon- Receptor 1 to Interferon- by Computer-Aided Design

Mikulecký, Pavel, Černý, Jiří, Biedermannová, Lada, Petroková, Hana, Kuchař, Milan, Vondrášek, Jiří, Malý, Petr, Šebo, Peter, Schneider, Bohdan

Journal:

BioMed Research International

Year:

2013

Language:

english

File:

PDF, 924 KB

english, 2013

49

Hypertrophic cardiomyopathy: from mutation to functional analysis of defective protein

Capek, Pavel, Vondrasek, Jiri, Skvor, Jiri, Brdicka, Radim

Journal:

Croatian Medical Journal

Year:

2011

Language:

english

File:

PDF, 402 KB

english, 2011

50

Trypsin- and Chymotrypsin-Like Serine Proteases in Schistosoma mansoni – ‘The Undiscovered Country’

Horn, Martin, Fajtová, Pavla, Rojo Arreola, Liliana, Ulrychová, Lenka, Bartošová-Sojková, Pavla, Franta, Zdeněk, Protasio, Anna V., Opavský, David, Vondrášek, Jiří, McKerrow, James H., Mareš, Michael,

Journal:

PLoS Neglected Tropical Diseases

Year:

2014

Language:

english

File:

PDF, 1.41 MB

english, 2014

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