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Works (18)

Design of Zn‐Binding Peptide(s) from Protein Fragments

ChemBioChem
2025-02-26 | Journal article
DOI: 10.1002/cbic.202401014
Contributors: Ján Michael Kormaník; Daniel Herman; Erik Andris; Martin Culka; Ondrej Gutten; Milan Kožíšek; Lucie Bednárová; Pavel Srb; Václav Veverka; Lubomír Rulíšek
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What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments

Chemical Science
2024 | Journal article
DOI: 10.1039/D3SC04960D
Contributors: Zuzana Osifová; Tadeáš Kalvoda; Jakub Galgonek; Martin Culka; Jiří Vondrášek; Petr Bouř; Lucie Bednárová; Valery Andrushchenko; Martin Dračínský; Lubomír Rulíšek
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Enzymatic Birch Reduction via Hydrogen Atom Transfer at an Aqua-Tungsten-bis-Metallopterin Cofactor

ACS Catalysis
2023-07-07 | Journal article
DOI: 10.1021/acscatal.3c01781
Contributors: Carola S. Seelmann; Simona G. Huwiler; Martin Culka; Marc J. F. Strampraad; Till Biskup; Stefan Weber; G. Matthias Ullmann; Volker Schünemann; Peter-Leon Hagedoorn; Antonio J. Pierik et al.
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Understanding desaturation/hydroxylation activity of castor stearoyl Δ9-Desaturase through rational mutagenesis

Computational and Structural Biotechnology Journal
2022 | Journal article
DOI: 10.1016/j.csbj.2022.03.010
Contributors: Michal Tupec; Martin Culka; Aleš Machara; Stanislav Macháček; Daniel Bím; Aleš Svatoš; Lubomír Rulíšek; Iva Pichová
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Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method

The Journal of Physical Chemistry B
2022-08-18 | Journal article
DOI: 10.1021/acs.jpcb.2c02861
Contributors: Tadeáš Kalvoda; Martin Culka; Lubomír Rulíšek; Erik Andris
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Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II

The Journal of Physical Chemistry B
2022-01-13 | Journal article
DOI: 10.1021/acs.jpcb.1c09240
Contributors: Daniel Bím; Michal Navrátil; Ondrej Gutten; Jan Konvalinka; Zsófia Kutil; Martin Culka; Václav Navrátil; Anastassia N. Alexandrova; Cyril Bařinka; Lubomír Rulíšek
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Mapping Conformational Space of All 8000 Tripeptides by Quantum Chemical Methods: What Strain Is Affordable within Folded Protein Chains?

The Journal of Physical Chemistry B
2021-01-14 | Journal article
DOI: 10.1021/acs.jpcb.0c09251
Contributors: Martin Culka; Tadeáš Kalvoda; Ondrej Gutten; Lubomír Rulíšek
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Dinucleoside Polyphosphates as RNA Building Blocks with Pairing Ability in Transcription Initiation

ACS Chemical Biology
2020-07-17 | Journal article
DOI: 10.1021/acschembio.0c00178
Contributors: Roberto Benoni; Martin Culka; Oldřich Hudeček; Lenka Gahurova; Hana Cahová
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Proton–Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase

Journal of the American Chemical Society
2020-06-10 | Journal article
DOI: 10.1021/jacs.0c01786
Contributors: Daniel Bím; Jakub Chalupský; Martin Culka; Edward I. Solomon; Lubomír Rulíšek; Martin Srnec
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Interplay between Conformational Strain and Intramolecular Interaction in Protein Structures: Which of Them Is Evolutionarily Conserved?

The Journal of Physical Chemistry B
2020-04-23 | Journal article
DOI: 10.1021/acs.jpcb.9b11784
Contributors: Martin Culka; Lubomír Rulíšek
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Dinucleoside polyphosphates act as 5′-RNA caps in bacteria

Nature Communications
2020-02-26 | Journal article
DOI: 10.1038/s41467-020-14896-8
Contributors: Oldřich Hudeček; Roberto Benoni; Paul E. Reyes-Gutierrez; Martin Culka; Hana Šanderová; Martin Hubálek; Lubomír Rulíšek; Josef Cvačka; Libor Krásný; Hana Cahová
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Factors Stabilizing β-Sheets in Protein Structures from a Quantum-Chemical Perspective

The Journal of Physical Chemistry B
2019-08-01 | Journal article
DOI: 10.1021/acs.jpcb.9b04866
Contributors: Martin Culka; Lubomír Rulíšek
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Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective

The Journal of Physical Chemistry B
2019-02-14 | Journal article
DOI: 10.1021/acs.jpcb.8b09245
Contributors: Martin Culka; Jakub Galgonek; Jiří Vymětal; Jiří Vondrášek; Lubomír Rulíšek
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Computational Biochemistry—Enzyme Mechanisms Explored

Structural and Mechanistic Enzymology
2017 | Other
DOI: 10.1016/bs.apcsb.2017.04.004
Contributors: Martin Culka; Florian J. Gisdon; G. Matthias Ullmann
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Martin Culka via Crossref Metadata Search

Breaking Benzene Aromaticity - Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase

Journal of the American Chemical Society
2017-09 | Journal article
DOI: 10.1021/jacs.7b07012
Contributors: Martin Culka; Simona G. Huwiler; Matthias Boll; G. Matthias Ullmann
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Martin Culka via Crossref Metadata Search
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Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF

Scientific Reports
2017-07-24 | Journal article
DOI: 10.1038/s41598-017-06278-w
Contributors: Christina Diederich; Mario Leypold; Martin Culka; Hansjörg Weber; Rolf Breinbauer; G. Matthias Ullmann; Wulf Blankenfeldt
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PyCPR – a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures

Journal of Molecular Modeling
2016-09 | Journal article
DOI: 10.1007/s00894-016-3116-8
Contributors: Florian J. Gisdon; Martin Culka; G. Matthias Ullmann
Source: Self-asserted source
Martin Culka via Crossref Metadata Search

Ferrous and ferric state of cytochromes P450 in intact Escherichia coli cells: a possible role of cytochrome P450-flavodoxin interactions.

2015 | Journal article
PMID: 26757119
Contributors: Culka M; Milichovsky J; Jerabek P; Stiborova M; Martinek V
Source: Self-asserted source
Martin Culka via Europe PubMed Central

Peer review (1 review for 1 publication/grant)

Review activity for The journal of physical chemistry. (1)
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