Author

Jochem H. Smit

University of GroningenORCID 0000-0002-3597-9429Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Research Focus:software / tool· 2 Organism:bacteria (other)· 1 Organism:E. coli· 1 Assay:imaging· 1 Assay:proteomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Anastassios EconomouiD· 2 shared Bindu Y. SrinivasuiD· 2 shared Rinky D. ParakraiD· 2 shared Spyridoula Karamanou AiD· 2 shared Thorben CordesiD· 2 shared Andreas HerrmanniD· 1 shared Athina G. PortaliouiD· 1 shared Biao YuaniD· 1 shared

Activity by Year

2019-2021 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersBioinformatics

Anastassios EconomouORCID

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Author profile →

3 papers

Recent·Most cited

Probing universal protein dynamics using residue-level Gibbs free energy

Jochem H. Smit, Srinath Krishnamurthy, Bindu Y. Srinivasu, Rinky D. Parakra, Spyridoula Karamanou A, Anastassios Economou

The paper introduces PyHDX, a tool for analyzing HDX-MS data to compute residue-level Gibbs free energy across protein conditions and homologues.

Analytical Chemistry · Sep 15, 2021Peer-reviewedBioinformatics

Structural dynamics of the functional nonameric Type III translocase export gate

Biao Yuan, Athina G. Portaliou, Rinky Parakra, Jochem H. Smit, Jiri Wald, Yichen Li, Bindu Y. Srinivasu, Maria S. Loos, Harveer Singh Dhupar, Dirk Fahrenkamp, Charalampos G. Kalodimos, Franck Duong, Thorben Cordes, Spyridoula Karamanou A, Thomas C. Marlovits, Anastassios Economou

The paper investigates the structural dynamics of SctV, a component of the Type III translocase export gate in E. coli, revealing its conformational changes and interactions with chaperones and ATPase.

Journal of Molecular Biology · Aug 26, 2021Peer-reviewedMolecular Biology

ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data

Jochem H. Smit, Yi‐Chen Li, Eliza M. Warszawik, Andreas Herrmann, Thorben Cordes

ColiCoords is a Python package that analyzes bacterial fluorescence microscopy data by transforming Cartesian coordinates to cellular coordinates, enabling statistical analysis of single-cell data.

PLoS ONE · Jun 19, 2019Peer-reviewedBioinformatics