Publications by authors named "Martin Culka"

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Design of Zn-Binding Peptide(s) from Protein Fragments.
Ján Michael Kormaník, Daniel Herman, Erik Andris, Martin Culka, Ondrej Gutten

Chembiochem· April 2025

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Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities.
Claire Simpson, Evgeniy Tabatsky, Zainab Rahil, Devon J Eddins, Sasha Tkachev, Martin Culka

Gigascience· January 2025

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Elucidation of factors shaping reactivity of 5'-deoxyadenosyl - a prominent organic radical in biology.
Zuzanna Wojdyla, Mauricio Maldonado-Domínguez, Priyam Bharadwaz, Martin Culka, Martin Srnec

Phys Chem Chem Phys· July 2024

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What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments.
Zuzana Osifová, Tadeáš Kalvoda, Jakub Galgonek, Martin Culka, Jiří Vondrášek

Chem Sci· January 2024

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Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method.
Tadeáš Kalvoda, Martin Culka, Lubomír Rulíšek, Erik Andris

J Phys Chem B· August 2022

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Evidence for H-bonding interactions to the μ-η:η-peroxide of oxy-tyrosinase that activate its coupled binuclear copper site.
Ioannis Kipouros, Agnieszka Stańczak, Martin Culka, Erik Andris, Timothy R Machonkin

Chem Commun (Camb)· March 2022

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Understanding desaturation/hydroxylation activity of castor stearoyl Δ-Desaturase through rational mutagenesis.
Michal Tupec, Martin Culka, Aleš Machara, Stanislav Macháček, Daniel Bím

Comput Struct Biotechnol J· March 2022

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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.
Daniel Bím, Michal Navrátil, Ondrej Gutten, Jan Konvalinka, Zsófia Kutil, Martin Culka

J Phys Chem B· January 2022

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Mapping Conformational Space of All 8000 Tripeptides by Quantum Chemical Methods: What Strain Is Affordable within Folded Protein Chains?
Martin Culka, Tadeáš Kalvoda, Ondrej Gutten, Lubomír Rulíšek

J Phys Chem B· January 2021

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Dinucleoside Polyphosphates as RNA Building Blocks with Pairing Ability in Transcription Initiation.
Roberto Benoni, Martin Culka, Oldřich Hudeček, Lenka Gahurova, Hana Cahová

ACS Chem Biol· July 2020

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Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ-Desaturase.
Daniel Bím, Jakub Chalupský, Martin Culka, Edward I Solomon, Lubomír Rulíšek

J Am Chem Soc· June 2020

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Interplay between Conformational Strain and Intramolecular Interaction in Protein Structures: Which of Them Is Evolutionarily Conserved?
Martin Culka, Lubomír Rulíšek

J Phys Chem B· April 2020

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Dinucleoside polyphosphates act as 5'-RNA caps in bacteria.
Oldřich Hudeček, Roberto Benoni, Paul E Reyes-Gutierrez, Martin Culka, Hana Šanderová

Nat Commun· February 2020

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Preparation of (Pentafluorosulfanyl)benzenes by Direct Fluorination of Diaryldisulfides: Synthetic Approach and Mechanistic Aspects.
Javier Ajenjo, Blanka Klepetářová, Martin Greenhall, Daniel Bím, Martin Culka

Chemistry· August 2019

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Factors Stabilizing β-Sheets in Protein Structures from a Quantum-Chemical Perspective.
Martin Culka, Lubomír Rulíšek

J Phys Chem B· August 2019

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Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective.
Martin Culka, Jakub Galgonek, Jiří Vymětal, Jiří Vondrášek, Lubomír Rulíšek

J Phys Chem B· February 2019

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Computational Biochemistry-Enzyme Mechanisms Explored.
Martin Culka, Florian J Gisdon, G Matthias Ullmann

Adv Protein Chem Struct Biol· November 2017

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Breaking Benzene Aromaticity-Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase.
Martin Culka, Simona G Huwiler, Matthias Boll, G Matthias Ullmann

J Am Chem Soc· October 2017

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Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF.
Christina Diederich, Mario Leypold, Martin Culka, Hansjörg Weber, Rolf Breinbauer

Sci Rep· July 2017

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PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.
Florian J Gisdon, Martin Culka, G Matthias Ullmann

J Mol Model· October 2016

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Ferrous and ferric state of cytochromes P450 in intact Escherichia coli cells: a possible role of cytochrome P450-flavodoxin interactions.
Martin Culka, Jan Milichovsky, Petr Jerabek, Marie Stiborova, Vaclav Martinek

Neuro Endocrinol Lett· April 2016

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