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Mokhosoev IM, Astakhov DV, Terentiev AA, Moldogazieva NT. Cytochrome P450 monooxygenase systems: Diversity and plasticity for adaptive stress response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 193:19-34. [PMID: 39245215 DOI: 10.1016/j.pbiomolbio.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/21/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions.
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Affiliation(s)
| | - Dmitry V Astakhov
- Department of Biochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia
| | - Alexander A Terentiev
- Department of Biochemistry and Molecular Biology, N.I. Pirogov Russian National Research Medical University, 117997, Moscow, Russia
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2
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Procházka D, Slanináková T, Olha J, Rošinec A, Grešová K, Jánošová M, Čillík J, Porubská J, Svobodová R, Dohnal V, Antol M. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic Acids Res 2024; 52:W182-W186. [PMID: 38747341 PMCID: PMC11223785 DOI: 10.1093/nar/gkae397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 07/06/2024] Open
Abstract
AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.
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Affiliation(s)
- David Procházka
- Faculty of Informatics, Masaryk University, Botanická 68A, Brno 60200, Czech Republic
| | - Terézia Slanináková
- Faculty of Informatics, Masaryk University, Botanická 68A, Brno 60200, Czech Republic
- Institute of Computer Science, Masaryk University, Šumavská 416/15, Brno 60200, Czech Republic
| | - Jaroslav Olha
- Faculty of Informatics, Masaryk University, Botanická 68A, Brno 60200, Czech Republic
- Institute of Computer Science, Masaryk University, Šumavská 416/15, Brno 60200, Czech Republic
| | - Adrián Rošinec
- Institute of Computer Science, Masaryk University, Šumavská 416/15, Brno 60200, Czech Republic
- Biological Data Management and Analysis Core Facility, CEITEC—Central European Institute of Technology, Masaryk University, Studentská, Brno 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Katarína Grešová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Miriama Jánošová
- Faculty of Informatics, Masaryk University, Botanická 68A, Brno 60200, Czech Republic
| | - Jakub Čillík
- Institute of Computer Science, Masaryk University, Šumavská 416/15, Brno 60200, Czech Republic
| | - Jana Porubská
- Biological Data Management and Analysis Core Facility, CEITEC—Central European Institute of Technology, Masaryk University, Studentská, Brno 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Radka Svobodová
- Biological Data Management and Analysis Core Facility, CEITEC—Central European Institute of Technology, Masaryk University, Studentská, Brno 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Vlastislav Dohnal
- Faculty of Informatics, Masaryk University, Botanická 68A, Brno 60200, Czech Republic
| | - Matej Antol
- Faculty of Informatics, Masaryk University, Botanická 68A, Brno 60200, Czech Republic
- Institute of Computer Science, Masaryk University, Šumavská 416/15, Brno 60200, Czech Republic
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3
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Wiley AM, Yang J, Madhani R, Nath A, Totah RA. Investigating the association between CYP2J2 inhibitors and QT prolongation: a literature review. Drug Metab Rev 2024; 56:145-163. [PMID: 38478383 DOI: 10.1080/03602532.2024.2329928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Drug withdrawal post-marketing due to cardiotoxicity is a major concern for drug developers, regulatory agencies, and patients. One common mechanism of cardiotoxicity is through inhibition of cardiac ion channels, leading to prolongation of the QT interval and sometimes fatal arrythmias. Recently, oxylipin signaling compounds have been shown to bind to and alter ion channel function, and disruption in their cardiac levels may contribute to QT prolongation. Cytochrome P450 2J2 (CYP2J2) is the predominant CYP isoform expressed in cardiomyocytes, where it oxidizes arachidonic acid to cardioprotective epoxyeicosatrienoic acids (EETs). In addition to roles in vasodilation and angiogenesis, EETs bind to and activate various ion channels. CYP2J2 inhibition can lower EET levels and decrease their ability to preserve cardiac rhythm. In this review, we investigated the ability of known CYP inhibitors to cause QT prolongation using Certara's Drug Interaction Database. We discovered that among the multiple CYP isozymes, CYP2J2 inhibitors were more likely to also be QT-prolonging drugs (by approximately 2-fold). We explored potential binding interactions between these inhibitors and CYP2J2 using molecular docking and identified four amino acid residues (Phe61, Ala223, Asn231, and Leu402) predicted to interact with QT-prolonging drugs. The four residues are located near the opening of egress channel 2, highlighting the potential importance of this channel in CYP2J2 binding and inhibition. These findings suggest that if a drug inhibits CYP2J2 and interacts with one of these four residues, then it may have a higher risk of QT prolongation and more preclinical studies are warranted to assess cardiovascular safety.
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Affiliation(s)
- Alexandra M Wiley
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Jade Yang
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rivcka Madhani
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
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4
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Chen EA, Porter LL. SSDraw: Software for generating comparative protein secondary structure diagrams. Protein Sci 2023; 32:e4836. [PMID: 37953705 PMCID: PMC10680343 DOI: 10.1002/pro.4836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/18/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
The program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring. Diagrams of homologous proteins can be registered according to an input multiple sequence alignment. Linear visualization allows the user to stack registered diagrams, facilitating comparison of secondary structure and other properties among homologous proteins. SSDraw can be used to compare secondary structures of homologous proteins with both conserved and divergent folds. It can also generate one secondary structure diagram from an input protein structure of interest. The source code can be downloaded (https://github.com/ncbi/SSDraw) and run locally for rapid structure generation, while a Google Colab notebook allows easy use.
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Affiliation(s)
- Ethan A. Chen
- National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaMarylandUSA
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
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5
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Dratch B, McWhorter KL, Blue TC, Jones SK, Horwitz SM, Davis KM. Insights into Substrate Recognition by the Unusual Nitrating Enzyme RufO. ACS Chem Biol 2023; 18:1713-1718. [PMID: 37555759 PMCID: PMC10442852 DOI: 10.1021/acschembio.3c00328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
Nitration reactions are crucial for many industrial syntheses; however, current protocols lack site specificity and employ hazardous chemicals. The noncanonical cytochrome P450 enzymes RufO and TxtE catalyze the only known direct aromatic nitration reactions in nature, making them attractive model systems for the development of analogous biocatalytic and/or biomimetic reactions that proceed under mild conditions. While the associated mechanism has been well-characterized in TxtE, much less is known about RufO. Herein we present the first structure of RufO alongside a series of computational and biochemical studies investigating its unusual reactivity. We demonstrate that free l-tyrosine is not readily accepted as a substrate despite previous reports to the contrary. Instead, we propose that RufO natively modifies l-tyrosine tethered to the peptidyl carrier protein of a nonribosomal peptide synthetase encoded by the same biosynthetic gene cluster and present both docking and molecular dynamics simulations consistent with this hypothesis. Our results expand the scope of direct enzymatic nitration reactions and provide the first evidence for such a modification of a peptide synthetase-bound substrate. Both of these insights may aid in the downstream development of biocatalytic approaches to synthesize rufomycin analogues and related drug candidates.
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Affiliation(s)
- Benjamin
D. Dratch
- Department of Chemistry, Emory
University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Kirklin L. McWhorter
- Department of Chemistry, Emory
University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | | | | | - Samantha M. Horwitz
- Department of Chemistry, Emory
University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Katherine M. Davis
- Department of Chemistry, Emory
University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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6
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Chamboko CR, Veldman W, Tata RB, Schoeberl B, Tastan Bishop Ö. Human Cytochrome P450 1, 2, 3 Families as Pharmacogenes with Emphases on Their Antimalarial and Antituberculosis Drugs and Prevalent African Alleles. Int J Mol Sci 2023; 24:ijms24043383. [PMID: 36834793 PMCID: PMC9961538 DOI: 10.3390/ijms24043383] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Precision medicine gives individuals tailored medical treatment, with the genotype determining the therapeutic strategy, the appropriate dosage, and the likelihood of benefit or toxicity. Cytochrome P450 (CYP) enzyme families 1, 2, and 3 play a pivotal role in eliminating most drugs. Factors that affect CYP function and expression have a major impact on treatment outcomes. Therefore, polymorphisms of these enzymes result in alleles with diverse enzymatic activity and drug metabolism phenotypes. Africa has the highest CYP genetic diversity and also the highest burden of malaria and tuberculosis, and this review presents current general information on CYP enzymes together with variation data concerning antimalarial and antituberculosis drugs, while focusing on the first three CYP families. Afrocentric alleles such as CYP2A6*17, CYP2A6*23, CYP2A6*25, CYP2A6*28, CYP2B6*6, CYP2B6*18, CYP2C8*2, CYP2C9*5, CYP2C9*8, CYP2C9*9, CYP2C19*9, CYP2C19*13, CYP2C19*15, CYP2D6*2, CYP2D6*17, CYP2D6*29, and CYP3A4*15 are implicated in diverse metabolic phenotypes of different antimalarials such as artesunate, mefloquine, quinine, primaquine, and chloroquine. Moreover, CYP3A4, CYP1A1, CYP2C8, CYP2C18, CYP2C19, CYP2J2, and CYP1B1 are implicated in the metabolism of some second-line antituberculosis drugs such as bedaquiline and linezolid. Drug-drug interactions, induction/inhibition, and enzyme polymorphisms that influence the metabolism of antituberculosis, antimalarial, and other drugs, are explored. Moreover, a mapping of Afrocentric missense mutations to CYP structures and a documentation of their known effects provided structural insights, as understanding the mechanism of action of these enzymes and how the different alleles influence enzyme function is invaluable to the advancement of precision medicine.
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Affiliation(s)
- Chiratidzo R Chamboko
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Rolland Bantar Tata
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Birgit Schoeberl
- Translational Medicine, Novartis Institutes for BioMedical Research, 220 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
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7
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Midlik A, Vařeková IH, Hutař J, Chareshneu A, Berka K, Svobodová R. OverProt: secondary structure consensus for protein families. Bioinformatics 2022; 38:3648-3650. [PMID: 35674374 DOI: 10.1093/bioinformatics/btac384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/24/2022] [Accepted: 06/05/2022] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the SSE type, length, frequency of occurrence, spatial variability, and β-connectivity. AVAILABILITY AND IMPLEMENTATION OverProt Server is freely available at https://overprot.ncbr.muni.cz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Adam Midlik
- CEITEC-Central European Institute of Technology, Masaryk University, Czech Republic 625 00 Brno.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Czech Republic 625 00 Brno
| | - Ivana Hutařová Vařeková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Czech Republic 625 00 Brno.,Faculty of Informatics, Masaryk University, Czech Republic 602 00 Brno.,Department of Physical Chemistry, Faculty of Science, Palacký University, Czech Republic 771 46 Olomouc
| | - Jan Hutař
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Czech Republic 625 00 Brno
| | - Aliaksei Chareshneu
- CEITEC-Central European Institute of Technology, Masaryk University, Czech Republic 625 00 Brno.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Czech Republic 625 00 Brno
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University, Czech Republic 771 46 Olomouc
| | - Radka Svobodová
- CEITEC-Central European Institute of Technology, Masaryk University, Czech Republic 625 00 Brno.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Czech Republic 625 00 Brno
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8
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Koulgi S, Jani V, Phukan S, Sonavane U, Joshi R, Kamboj RK, Palle V. A Deep Dive into the Conformational Dynamics of CYP3A4 : Understanding the Binding of Homotropic and Non‐homotropic Ligands for Mitigating Drug‐Drug interaction (DDI). ChemistrySelect 2022. [DOI: 10.1002/slct.202200249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shruti Koulgi
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Vinod Jani
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Samiron Phukan
- Lupin Limited (Research Park), Nande Village Pune 412115 India
| | - Uddhavesh Sonavane
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Rajendra Joshi
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | | | - Venkata Palle
- Lupin Limited (Research Park), Nande Village Pune 412115 India
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9
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Hutařová Vařeková I, Hutař J, Midlik A, Horský V, Hladká E, Svobodová R, Berka K. 2DProts: Database of Family-Wide Protein Secondary Structure Diagrams. Bioinformatics 2021; 37:4599-4601. [PMID: 34244700 PMCID: PMC8652034 DOI: 10.1093/bioinformatics/btab505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/28/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
Summary Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. Availability and Implementation Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ivana Hutařová Vařeková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.,Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Jan Hutař
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Adam Midlik
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Vladimír Horský
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Eva Hladká
- Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Radka Svobodová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, 771 46, Czech Republic
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