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 at Lessingstraße 8, Seminar Room 113, every Tuesday from 10.04.2018 – 13.07.2018 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.

Schedule

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

Paper Pile

2018

Boiteau, Rene; Hoyt, David; Nicora, Carrie; Kinmonth-Schultz, Hannah; Ward, Joy; Bingol, Kerem

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction Journal Article

Metabolites, 8 (1), pp. 8, 2018.

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

2017

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

Patiny, Luc; "e, Micha; Kostro, Daniel; Bernal, Andrés; Castillo, Andrés M; ~n, Alejandro Bola; Asencio, Miguel A; Pellet, Norman; Todd, Matthew; Schloerer, Nils; Kuhn, Stefan; Holmes, Elaine; Javor, Sacha; Wist, Julien

The C6H6 NMR repository: An integral solution to control the flow of your data from the magnet to the public Journal Article

Magnetic Resonance in Chemistry, 3 (D1), pp. 160018, 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

Blin, Kai; Wolf, Thomas; Chevrette, Marc G; Lu, Xiaowen; Schwalen, Christopher J; Kautsar, Satria A; Duran, Hernando Suarez G; de los Santos, Emmanuel L C; Kim, Hyun Uk; Nave, Mariana; Dickschat, Jeroen S; Mitchell, Douglas A; Shelest, Ekaterina; Breitling, Rainer; Takano, Eriko; Lee, Sang Yup; Weber, Tilmann; Medema, Marnix H

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification Journal Article

Nucleic Acids Research, 45 (W1), pp. W36–W41, 2017.

Links | BibTeX

2014

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

2008

Ertl, Peter; Roggo, Silvio; Schuffenhauer, Ansgar

Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Journal Article

Journal of Chemical Information and Modeling, 48 (1), pp. 68-74, 2008, (PMID: 18034468).

Links | BibTeX

1997

Schriber, H; Pretsch, E

Rule-based system to derive automatically good-list and bad- list entries for structures generators from spectra Journal Article

Journal of Chemical Information & Computer Sciences, 37 (5), pp. 884–891, 1997.

Links | BibTeX

1996

Will, M; Fachinger, W; Richert, JR

Fully automated structure elucidation - A spectroscopist's dream comes true Journal Article

Journal of Chemical Information & Computer Sciences, 36 (2), pp. 221–227, 1996.

Abstract | Links | BibTeX

1992

Faulon, J L

On Using Graph-Equivalent Classes for the Structure Elucidation of Large Molecules Journal Article

Journal of Chemical Information & Computer Sciences, 32 (4), pp. 338–348, 1992.

Links | BibTeX

1965

Morgan, H L

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

J. Chem. Doc., 5 , pp. 107–113, 1965.

BibTeX