Prof Dr Olga Kalinina
About
Olga Kalinina received a M.Sc. degree with distinction in mathematics from the Moscow State University in 2003 and a Ph.D. from the Engelhardt Institute for Molecular Biology of the Russian Academy of Sciences in 2007. She continued her research in bioinformatics as a postdoctoral fellow at the European Laboratory for Molecular Biology, for which she was awarded an EMBO Long Term Fellowship from the European Molecular Biology Organization, and later at the University of Heidelberg, working with Prof. Dr. Robert B. Russell (2007-2011). In 2012, she established her independent junior group at the Max Planck Institute for Informatics in the Department for Computational Biology and Applied Algorithmics lead by Prof. Dr. Dr. Thomas Lengauer, where she was researching resistance mechanisms in human viruses until 2018.
2024
The Peptide Antibiotic Corramycin Adopts a β-Hairpin-like Structure and Is Inactivated by the Kinase ComG
Adam S, Fries F, Tesmar A, Rasheed S, Deckarm S, Sousa C, Reberšek R, Risch T, Mancini S, Herrmann J, …, Kalinina O, Müller R (2024)
J. Am. Chem. Soc.DOI: 10.1021/jacs.3c13208
Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins
Fu C, Liu Y, Walt C, Rasheed S, Bader C, Lukat P, Neuber M, Haeckl F, Blankenfeldt W, Kalinina O, Müller R (2024)
Nat Commun 15 (1)DOI: 10.1038/s41467-024-44953-5
2023
Artificial intelligence for natural product drug discovery
Mullowney M, Duncan K, Elsayed S, Garg N, van der Hooft J, Martin N, Meijer D, Terlouw B, Biermann F, Blin K, …, Robinson S, Medema M (2023)
Nat Rev Drug DiscovDOI: 10.1038/s41573-023-00774-7
Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis
Adam S, Zheng D, Klein A, Volz C, Mullen W, Shirran S, Smith B, Kalinina O, Müller R, Koehnke J (2023)
Nature chemistry 15 (4): 560-568DOI: 10.1038/s41557-023-01153-w
Insights into the biosynthesis of icumazole, unveiling a distinctive family of crotonyl-CoA carboxylase/reductase
Xie F, Kiefer A, Hirsch A, Kalinina O, Fu C, Müller R (2023)
Cell Reports Physical Science 4 (5)DOI: 10.1016/j.xcrp.2023.101394
2020
A hydrogel-based in vitro assay for the fast prediction of antibiotic accumulation in Gram-negative bacteria
Richter R, Kamal M, García-Rivera M, Kaspar J, Junk M, Elgaher W, Srikakulam S, Gress A, Beckmann A, Grißmer A, …, Schneider-Daum N, Lehr C (2020)
Materials today. Bio 8DOI: 10.1016/j.mtbio.2020.100084
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
Mironov A, Denisov S, Gress A, Kalinina O, Pervouchine D (2020)
BookDOI: 10.1101/2020.09.11.292722
The bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes
Sikandar A, Franz L, Adam S, Santos-Aberturas J, Horbal L, Luzhetskyy A, Truman A, Kalinina O, Koehnke J (2020)
Nat Chem Biol 16 (9): 1013-1018DOI: 10.1038/s41589-020-0569-y
DIGGER: exploring the functional role of alternative splicing in protein interactions
Louadi Z, Yuan K, Gress A, Tsoy O, Kalinina O, Baumbach J, Kacprowski T, List M (2020)
Nucleic Acids ResDOI: 10.1093/nar/gkaa768
Frequent subgraph mining for biologically meaningful structural motifs
Keller S, Miettinen P, Kalinina O (2020)
BookDOI: 10.1101/2020.05.14.095695
SphereCon-a method for precise estimation of residue relative solvent accessible area from limited structural information
Gress A, Kalinina O (2020)
Bioinformatics (Oxford, England) 36 (11): 3372-3378DOI: 10.1093/bioinformatics/btaa159
Resistance-associated substitutions in patients with chronic hepatitis C virus genotype 4 infection
Dietz J, Kalinina O, Vermehren J, Peiffer K, Matschenz K, Buggisch P, Niederau C, Schattenberg J, Müllhaupt B, Yerly S, …, Welsch C, Sarrazin C (2020)
J. Viral Hepat.DOI: 10.1111/jvh.13322.
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors
Bastys T, Gapsys V, Walter H, Heger E, Doncheva N, Kaiser R, Groot B, Kalinina O (2020)
Retrovirology 17 (1)DOI: 10.1186/s12977-020-00520-6
A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance
Srikakulam S, Bastys T, Kalinina O (2020)
ProteinsDOI: 10.1002/prot.25963
2019
Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes
Ahmad M, Helms V, Kalinina O, Lengauer T (2019)
Journal of chemical theory and computation 15 (4): 2166-2178DOI: 10.1021/acs.jctc.8b01074
Adenosine-to-Inosine RNA Editing in Mouse and Human Brain Proteomes
Levitsky L, Kliuchnikova A, Kuznetsova K, Karpov D, Ivanov M, Pyatnitskiy M, Kalinina O, Gorshkov M, Moshkovskii S (2019)
Proteomics 19 (23)DOI: 10.1002/pmic.201900195.
Targeting actin inhibits repair of doxorubicin-induced DNA damage: a novel therapeutic approach for combination therapy
Pfitzer L, Moser C, Gegenfurtner F, Arner A, Foerster F, Atzberger C, Zisis T, Kubisch-Dohmen R, Busse J, Smith R, …, Vollmar A, Zahler S (2019)
Cell Death Dis. 10 (4)DOI: 10.1038/s41419-019-1546-9
2018
Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms
Knops E, Sierra S, Kalaghatgi P, Heger E, Kaiser R, Kalinina O (2018)
Genes 9 (7)DOI: 10.3390/genes9070343
Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations
Bastys T, Gapsys V, Doncheva N, Kaiser R, Groot B, Kalinina O (2018)
Journal of chemical theory and computation 14 (7): 3397-3408DOI: 10.1021/acs.jctc.7b01109
Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA
Sikandar A, Cirnski K, Testolin G, Volz C, Brönstrup M, Kalinina O, Müller R, Koehnke J (2018)
J. Am. Chem. Soc. 140 (48): 16641-16649DOI: 10.1021/jacs.8b08895
2017
Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes
Gress A, Ramensky V, Kalinina O (2017)
Oncogenesis 6 (9)DOI: 10.1038/oncsis.2017.79.
2016
Patterns of amino acid conservation in human and animal immunodeficiency viruses
Voitenko O, Dhroso A, Feldmann A, Korkin D, Kalinina O (2016)
Bioinformatics (Oxford, England) 32 (17): 685-DOI: 10.1093/bioinformatics/btw441
StructMAn: annotation of single-nucleotide polymorphisms in the structural context
Gress A, Ramensky V, Büch J, Keller A, Kalinina O (2016)
Nucleic Acids Res 44 (W1): 463-8DOI: 10.1093/nar/gkw364
BALL-SNPgp-from genetic variants toward computational diagnostics
Mueller S, Backes C, Gress A, Baumgarten N, Kalinina O, Moll A, Kohlbacher O, Meese E, Keller A (2016)
Bioinformatics (Oxford, England) 32 (12): 1888-90DOI: 10.1093/bioinformatics/btw084