In this seminar open to all students at the University of Jena (subject to subscribing via Fridolin) we are discussing current topics in Cheminformatics, which might involve discussing older papers if they are relevant. This is a seminar where active involvement by all participants at all occasions is assumed. Everyone will need to have read the paper *before* the seminar.

“Current Topics in Cheminformatics”  takes place during each lecture period at Lessingstraße 8, Seminar Room 113, every Tuesday from 10:15 to 11:45 o’ clock.

Please contact the organiser, christoph.steinbeck [at] uni [minus] jena [dot] de, if you are interested in participating.


Papers to be discussed are selected from the paper pile listed below. Please contact the organizer if you wish to add a paper to the pile.

Summer Semester 2020

Winter Semester (2019/20)

Summer Semester 2019

Winter Semester (2018/19)

Summer Semester (2018)

Paper Pile


Ricart, Emma; Pupin, Maude; Müller, Markus; Lisacek, Frédérique

Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products Journal Article

Analytical Chemistry, 2020, ISSN: 0003-2700.

Links | BibTeX

Rampler, Evelyn; Abiead, Yasin El; Schoeny, Harald; Rusz, Mate; Hildebrand, Felina; Fitz, Veronika; Koellensperger, Gunda

Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics—Standardization, Coverage, and Throughput Journal Article

Analytical Chemistry, 2020, ISSN: 0003-2700.

Links | BibTeX

Beard, Edward J; Cole, Jacqueline M

ChemSchematicResolver: A Toolkit to Decode 2D Chemical Diagrams with Labels and R-Groups into Annotated Chemical Named Entities Journal Article

Journal of Chemical Information and Modeling, 0 (0), pp. null, 2020, (PMID: 32212690).

Links | BibTeX

Reher, Raphael; Kim, Hyun Woo; Zhang, Chen; Mao, Huanru Henry; Wang, Mingxun; Nothias, Louis-Félix; Caraballo-Rodriguez, Andres Mauricio; Glukhov, Evgenia; Teke, Bahar; Leao, Tiago; Alexander, Kelsey L; Duggan, Brendan M; Everbroeck, Ezra Van L; Dorrestein, Pieter C; Cottrell, Garrison W; Gerwick, William H

A Convolutional Neural Network-Based Approach for the Rapid Characterization of Molecularly Diverse Natural Products Journal Article Forthcoming

Journal of the American Chemical Society, 0 (ja), pp. null, Forthcoming, (PMID: 32045230).

Links | BibTeX

Stumpfe, Dagmar; Bajorath, Jürgen

Current Trends, Overlooked Issues, and Unmet Challenges in Virtual Screening Journal Article

Journal of Chemical Information and Modeling, 2020, ISSN: 1549-9596.

Abstract | Links | BibTeX

Kwon, Youngchun; Lee, Dongseon; Choi, Youn-Suk; Shin, Kyoham; Kang, Seokho

Compressed graph representation for scalable molecular graph generation Journal Article

Journal of Cheminformatics, 2020, ISSN: 1758-2946.

Abstract | Links | BibTeX

Desmet, Sandrien; Brouckaert, Marlies; Morreel, Kris; Boerjan, Wout

Seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks Journal Article

Computational and Structural Biotechnology Journal, 2020, ISSN: 2001-0370.

Abstract | Links | BibTeX


Djoumbou-Feunang, Yannick; Pon, Allison; Karu, Naama; Zheng, Jiamin; Li, Carin; Arndt, David; Gautam, Maheswor; Allen, Felicity; Wishart, David S

CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification Journal Article

Metabolites, 9 (4), 2019, ISSN: 2218-1989.

Abstract | Links | BibTeX

Ji, Hongchao; Xu, Yamei; Lu, Hongmei; Zhang, Zhimin

Deep MS/MS-Aided Structural-Similarity Scoring for Unknown Metabolite Identification Journal Article

Analytical Chemistry, 91 (9), pp. 5629–5637, 2019, ISSN: 15206882.

Abstract | Links | BibTeX


Kochev, Nikolay; Avramova, Svetlana; Jeliazkova, Nina

Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation Journal Article

Journal of Cheminformatics, 10 (1), pp. 42, 2018, ISSN: 1758-2946.

Abstract | Links | BibTeX

Kotov, Serhii; Tremouilhac, Pierre; Jung, Nicole; Bräse, Stefan

Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications Journal Article

Journal of Cheminformatics, 10 (1), pp. 38, 2018, ISSN: 1758-2946.

Abstract | Links | BibTeX

Hähnke, Volker D; Kim, Sunghwan; Bolton, Evan E

PubChem chemical structure standardization Journal Article

Journal of Cheminformatics, 10 (1), pp. 36, 2018, ISSN: 1758-2946.

Abstract | Links | BibTeX

Sivakumar, Tadi Venkata; Bhaduri, Anirban; Muni, Rajasekhara Reddy Duvvuru; Park, Jin Hwan; Kim, Tae Yong

SimCAL: a flexible tool to compute biochemical reaction similarity Journal Article

BMC Bioinformatics, 19 (1), pp. 254, 2018, ISSN: 1471-2105.

Abstract | Links | BibTeX

Blazenovic, Ivana; Kind, Tobias; Ji, Jian; Fiehn, Oliver

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics Journal Article

Metabolites, 8 (2), pp. 31, 2018.

Abstract | Links | BibTeX

Chong, Jasmine; Soufan, Othman; Li, Carin; Caraus, Iurie; Li, Shuzhao; Bourque, Guillaume; Wishart, David S; Xia, Jianguo

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis Journal Article

Nucleic Acids Research, 37 , pp. W652, 2018.

Abstract | Links | BibTeX

KG, Georg Thieme Verlag; Scossa, Federico; Benina, Maria; Alseekh, Saleh; Zhang, Youjun; Fernie, Alisdair R

The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants Journal Article

Planta Medica, (EFirst), 2018.

Abstract | Links | BibTeX

Tanaka, Wataru; Arita, Masanori

Physicochemical Prediction of Metabolite Fragmentation in Tandem Mass Spectrometry Journal Article

Mass Spectrometry, 7 (1), pp. A0066-A0066, 2018.

Links | BibTeX


Lai, Zijuan; Tsugawa, Hiroshi; Wohlgemuth, Gert; Mehta, Sajjan; Mueller, Matthew; Zheng, Yuxuan; Ogiwara, Atsushi; Meissen, John; Showalter, Megan; Takeuchi, Kohei; Kind, Tobias; Beal, Peter; Arita, Masanori; Fiehn, Oliver

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics Journal Article

Nature Methods, 122 (1), pp. 769–56, 2017.

Abstract | Links | BibTeX

Alden, Nicholas; Krishnan, Smitha; Porokhin, Vladimir; Raju, Ravali; McElearney, Kyle; Gilbert, Alan; Lee, Kyongbum

Biologically Consistent Annotation of Metabolomics Data Journal Article

Analytical Chemistry, 89 (24), pp. acs.analchem.7b02162–13104, 2017.

Abstract | Links | BibTeX

Naake, Thomas; Gaquerel, Emmanuel

MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data Journal Article

Bioinformatics, 33 (15), pp. 2419–2420, 2017.

Abstract | Links | BibTeX


Sahoo, Sagarika; Adhikari, Chandana; Mishra, Minati Kuanar; K., Bijay

A Short Review of the Generation of Molecular Descriptors and Their Applications in Quantitative Structure Property/Activity Relationships Journal Article

Current Computer-Aided Drug Design, 12 (3), pp. 181-205, 2016.

Links | BibTeX


Heller, Stephen R; McNaught, Alan; Pletnev, Igor; Stein, Stephen; Tchekhovskoi, Dmitrii

InChI, the IUPAC International Chemical Identifier Journal Article

Journal of Cheminformatics, 7 (1), pp. 23, 2015, ISSN: 1758-2946.

Abstract | Links | BibTeX


Willoughby, Patrick H; Jansma, Matthew J; Hoye, Thomas R

A guide to small-molecule structure assignment through computation of (1H and 13C) NMR chemical shifts Journal Article

Nature protocols, 9 (3), pp. 643–660, 2014.

Abstract | Links | BibTeX


Plainchont, Bertrand; de Emerenciano, Vicente Paulo; Nuzillard, Jean-Marc

Recent advances in the structure elucidation of small organic molecules by the LSD software Journal Article

Magnetic Resonance in Chemistry, 51 (8), pp. 447-453, 2013.

Abstract | Links | BibTeX

Heller, Stephen; McNaught, Alan; Stein, Stephen; Tchekhovskoi, Dmitrii; Pletnev, Igor

InChI - the worldwide chemical structure identifier standard Journal Article

Journal of Cheminformatics, 5 (1), pp. 7, 2013, ISSN: 1758-2946.

Abstract | Links | BibTeX


Schymanski, Emma L; Gallampois, Christine M J; Krauss, Martin; Meringer, Markus; Neumann, Steffen; Schulze, Tobias; Wolf, Sebastian; Brack, Werner

Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties Journal Article

Analytical Chemistry, 84 (7), pp. 3287-3295, 2012, (PMID: 22414024).

Links | BibTeX

Reymond, Jean-Louis; Ruddigkeit, Lars; Blum, Lorenz; van Deursen, Ruud

The enumeration of chemical space Journal Article

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2 (5), pp. 717-733, 2012.

Abstract | Links | BibTeX


Elyashberg, Mikhail E; Blinov, Kirill A; Williams, Antony J; Molodtsov, Sergey G; Martin, Gary E; Martirosian, Eduard R

Structure Elucidator:  A Versatile Expert System for Molecular Structure Elucidation from 1D and 2D NMR Data and Molecular Fragments Journal Article

Journal of Chemical Information and Computer Sciences, 44 (3), pp. 771-792, 2004, (PMID: 15154743).

Links | BibTeX


Schulz, K -P; Korytko, A; Munk, M E

Applications of a HOUDINI-Based Structure Elucidation System Journal Article

Journal of Chemical Information and Computer Sciences, 43 (5), pp. 1447-1456, 2003, (PMID: 14502477).

Links | BibTeX


Munk, Morton E

Computer-Based Structure Determination:  Then and Now Journal Article

Journal of Chemical Information and Computer Sciences, 38 (6), pp. 997-1009, 1998.

Links | BibTeX


Funatsu, Kimito; Sasaki, Shin-ichi

Recent Advances in the Automated Structure Elucidation System, CHEMICS. Utilization of Two-Dimensional NMR Spectral Information and Development of Peripheral Functions for Examination of Candidates Journal Article

Journal of Chemical Information and Computer Sciences, 36 (2), pp. 190-204, 1996.

Links | BibTeX


Peng, Chen; Yuan, Shengang; Zheng, Chongzhi; Hui, Yongzheng

Efficient Application of 2D NMR Correlation Information in Computer-Assisted Structure Elucidation of Complex Natural Products Journal Article

Journal of Chemical Information and Computer Sciences, 34 (4), pp. 805-813, 1994.

Links | BibTeX


Razinger, Marko; Balasubramanian, K; Munk, Morton

Graph automorphism perception algorithms in computer-enhanced structure elucidation Journal Article

Journal of chemical information and computer sciences, 33 , pp. 197-201, 1993.

Links | BibTeX


Gasteiger, J; Rudolph, C; Sadowski, J

Automatic generation of 3D-atomic coordinates for organic molecules Journal Article

Tetrahedron Computer Methodology, 3 (6, Part C), pp. 537 - 547, 1990, ISSN: 0898-5529, (Three-dimensional chemical structure handling).

Abstract | Links | BibTeX


Weininger, David; Weininger, Arthur; Weininger, Joseph L

SMILES. 2. Algorithm for generation of unique SMILES notation Journal Article

Journal of Chemical Information and Computer Sciences, 29 (2), pp. 97-101, 1989.

Links | BibTeX


Weininger, David

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules Journal Article

Journal of Chemical Information and Computer Sciences, 28 (1), pp. 31-36, 1988.

Links | BibTeX


Balaban, Alexandru T; Mekenyan, Ovanes; Bonchev, Danail

Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). I. Algorithms for finding graph orbits and canonical numbering of atoms Journal Article

Journal of Computational Chemistry, 6 (6), pp. 538-551, 1985.

Abstract | Links | BibTeX


Shelley, CraigA.; Munk, MortonE.

Case, a computer model of the structure elucidation process Journal Article

Analytica Chimica Acta, 133 (4), pp. 507 - 516, 1981, ISSN: 0003-2670.

Abstract | Links | BibTeX


Nourse, James G; Carhart, Raymond E; Smith, Dennis H; Djerassi, Carl

Applications of artificial intelligence for chemical inference. 29. Exhaustive generation of stereoisomers for structure elucidation Journal Article

Journal of the American Chemical Society, 101 (5), pp. 1216-1223, 1979.

Links | BibTeX


Woodruff, Hugh B; Snelling, Charles R; Shelley, Craig A; Munk, Morton

Computer-assisted interpretation of carbon-13 nuclear magnetic resonance spectra applied to structure elucidation of natural products Journal Article

Analytical Chemistry - ANAL CHEM, 49 , 1977.

Links | BibTeX


Ullmann, J R

An Algorithm for Subgraph Isomorphism Journal Article

J. ACM, 23 (1), pp. 31–42, 1976, ISSN: 0004-5411.

Links | BibTeX


Morgan, H L

The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. Journal Article

Journal of Chemical Documentation, 5 (2), pp. 107-113, 1965.

Links | BibTeX


Tanimoto, T T

An Elementary Mathematical theory of Classification and Prediction Journal Article

126 (3278), pp. 814–819, 1958.

Links | BibTeX


Ray, Louis C; Kirsch, Russell A

Finding Chemical Records by Digital Computers Journal Article

Science, 126 (3278), pp. 814–819, 1957, ISSN: 0036-8075.

Links | BibTeX


Wiener, Harry

Structural Determination of Paraffin Boiling Points Journal Article

Journal of the American Chemical Society, 69 (1), pp. 17-20, 1947, (PMID: 20291038).

Links | BibTeX