Publications

Publications

Original Journal Papers

2020–2021

  • T.-M. Dutschmann, K. Baumann, Evaluating High-Variance Leaves as Uncertainty Measure for Random Forest Regression, Molecules 2021, 26, 6541. DOI: 10.3390/molecules26216514
  • N. M. Francke, F. Schneider, K. Baumann, H. Bunjes, Formulation of Cannabidiol in Colloidal Lipid Carriers, Molecules 2021, 26, 1469. DOI: 10.3390/molecules26051469

2015–2019

  • C. Schmidt, L. Albrecht, S. Balasupramaniam, R. Misgeld, B. Karge, M. Brönstrup, A. Prokop, K. Baumann, S. Reichl, I. Ott, A gold(I) biscarbene complex with improved activity as a TrxR inhibitor and cytotoxic drug: comparative studies with different gold metallodrugs, Metallomics 2019, 11, 533–545. DOI: 10.1039/c8mt00306h

  • E. T. Bayat, B. Hemmateenejad, M. Akhond, M. M. Bordbar, K. Baumann, On the dependency between principal components: Application to determine the rank of a matrix in an evolutionary process, J. Chemom. 2019, 33, e3102. DOI: 10.1002/cem.3102

  • J. Dreher, J. Scheiber, N. Stiefl, Baumann K., xMaP—An Interpretable Alignment-Free Four-Dimensional Quantitative Structure–Activity Relationship Technique Based on Molecular Surface Properties and Conformer Ensembles, J. Chem. Inf. Model. 2018, 58, 165–181. DOI: 10.1021/acs.jcim.7b00419

  • L. Kalinowsky, J. Weber, S. Balasupramaniam, K. Baumann, E. Proschak, A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions, ACS Omega 2018, 3, 5704–5714. DOI: 10.1021/acsomega.7b01194

  • K. Göke, T. Lorenz, A. Repanas, F. Schneider, D. Steiner, K. Baumann, H. Bunjes, A. Dietzel, J. H. Finke, B. Glasmacher, A. Kwade, Novel strategies for the formulation and processing of poorly water-soluble drugs, Eur. J. Pharm. Biopharm. 2018, 126, 40–56. DOI: 10.1016/j.ejpb.2017.05.008
  • B. Hemmateenejad, K. Baumann, Screening for linearly and nonlinearly related variables in predictive cheminformatic models, J. Chemom. 2018, 32, e3009. DOI: 10.1002/cem.3009
  • W. Klingspohn, M. Mathea, A. ter Laak, N. Heinrich, K. Baumann, Efficiency of different measures for defining the applicability domain of classification models, J. Cheminf. 2017, 9, #44. DOI: 10.1186/s13321-017-0230-2
  • M. Mathea, W. Klingspohn, K. Baumann, Chemoinformatic Classification Methods and their Applicability Domain, Mol. Inf. 2016, 35, 160–180. DOI: 10.1002/minf.201501019

  • H. Wätzig, I. Oltmann-Norden, F. Steinicke, H. A. Alhazmi, M. Nachbar, D. A. El-Hady, H. M. Albishri, K. Baumann, T. Exner, F. M. Böckler, S. El Deeb, Data quality in drug discovery: the role of analytical performance in ligand binding assays, J. Comp.-Aided Mol. Design 2015, 29, 847–865. DOI: 10.1007/s10822-015-9851-6

  • H. Falke, A. Chaikuad, A. Becker, N. Loaëc, O. Lozach, S. Abu Jhaisha, W. Becker, P. G. Jones, L. Preu, K. Baumann, S. Knapp, L. Meijer, C. Kunick,10-Iodo-11H-indolo[3,2-c]quinoline-6-carboxylic Acids Are Selective Inhibitors of DYRK1A, J. Med. Chem. 2015, 58, 3131–3143. DOI: 10.1021/jm501994d
  • K. Schumacher, M. Matz, D. Brüning, K. Baumann, I. Rustenbeck, Granule Mobility, Fusion Frequency and Insulin Secretion Are Differentially Affected by Insulinotropic Stimuli, Traffic 2015, 16, 493–509. DOI: 10.1111/tra.12261

2010–2014

  • D. Baumann, K. Baumann, Reliable estimation of prediction errors for QSAR models under model uncertainty using double cross-validation, J. Cheminf. 2014, 6, #47. DOI: 10.1186/s13321-014-0047-1
  • S. Wollenhaupt, K. Baumann, inSARa: Intuitive and Interactive SAR Interpretation by Reduced Graphs and Hierarchical MCS-Based Network Navigation, J. Chem. Inf. Model. 2014, 54, 1578–1595. DOI: 10.1021/ci4007547

  • M. Matz, K. Schumacher, K. Hatlapatka, D. Lorenz, K. Baumann, I. Rustenbeck, Observer-Independent Quantification of Insulin Granule Exocytosis and Pre-Exocytotic Mobility by TIRF Microscopy, Microsc. Microanal. 2014, 20, 206–218. DOI: 10.1017/S1431927613013767

  • D. Saaber, S. Wollenhaupt, K. Baumann, S. Reichl, Recent progress in tight junction modulation for improving bioavailability, Exp. Opin. Drug Discov. 2014, 9, 367–381. DOI: 10.1517/17460441.2014.892070

  • L. Oehninger, M. Stefanopoulou, H. Alborzinia, J. Schur, S. Ludewig, K. Namikawa, A. Muñoz-Castro, R.W. Köster, K. Baumann, S. Wölfl, W.S. Sheldrick, I. Ott, Evaluation of arene ruthenium(II) N-heterocyclic carbene complexes as organometallics interacting with thiol and selenol containing biomolecules, Dalton Trans. 2013, 42, 1657–1666. DOI: 10.1039/c2dt32319b

  • R. Determann, J. Dreher, K. Baumann, L. Preu, P.G. Jones, F. Totzke, C. Schächtele, M.H.G. Kubbutat, C. Kunick, 2-Anilino-4-(benzimidazol-2-yl)pyrimidines – A multikinase inhibitor scaffold with antiproliferative activity toward cancer cell lines, Eur. J. Med. Chem. 2012, 53, 254–263. DOI: 10.1016/j.ejmech.2012.04.007

  • L. Oehninger, H. Alborzinia, S. Ludewig, K. Baumann, S. Woelfl, I. Ott, From Catalysts to Bioactive Organometallics: Do Grubbs Catalysts Trigger Biological Effects?, ChemMedChem 2011, 6, 2142–2145. DOI: 10.1002/cmdc.201100308

  • K. Hatlapatka, M. Matz, K. Schumacher, K. Baumann, I. Rustenbeck, Bidirectional Insulin Granule Turnover in the Submembrane Space During K+ Depolarization-Induced Secretion, Traffic 2011, 12, 1166–1178. DOI: 10.1111/j.1600-0854.2011.01231.x

  • S. Alban, S. Luehn, S. Schiemann, T. Beyer, J. Norwig, C. Schilling, O. Raedler, B. Wolf, M. Matz, K. Baumann, U. Holzgrabe, Comparison of established and novel purity tests for the quality control of heparin by means of a set of 177 heparin samples, Anal. Bioanal. Chem. 2011, 399, 605–620. DOI: 10.1007/s00216-010-4169-7

  • G. Bringmann, S.K. Bischof, S. Mueller, T. Gulder, C. Winter, A. Stich, H. Moll, M. Kaiser, R. Brun, J. Dreher, K. Baumann, QSAR guided synthesis of simplified antiplasmodial analogs of naphthylisoquinoline alkaloids, Eur. J. Med. Chem. 2010, 45, 5370–5383. DOI: 10.1016/j.ejmech.2010.08.062

  • T. Beyer, M. Matz, D. Brinz, O. Raedler, B. Wolf, J. Norwig, K. Baumann, S. Alban, U. Holzgrabe, Composition of OSCS-contaminated heparin occurring in 2008 in batches on the German market, Eur. J. Pharm. Sci. 2010, 40, 297–304. DOI: 10.1016/j.ejps.2010.04.002

  • A.-M. Egert-Schmidt, J. Dreher, U. Dunkel, S. Kohfeld, L. Preu, H. Weber, J. E. Ehlert, B. Mutschler, F. Totzke, C. Schächtele, M. H. G. Kubbutat, K. Baumann, C. Kunick, Identification of 2-Anilino-9-methoxy-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepin-6-ones as Dual PLK1/VEGF-R2 Kinase Inhibitor Chemotypes by Structure-Based Lead Generation, J. Med. Chem. 2010, 53, 2433–2442. DOI: 10.1021/jm901388c

  • S. Ludewig, M. Kossner, M. Schiller, K. Baumann, T. Schirmeister, Enzyme Kinetics and Hit Validation in Fluorimetric Protease Assays, Curr. Top. Med. Chem. 2010, 10, 368–382. DOI: 10.2174/156802610790725498

2005–2009

  • U. Schmid, P. Rösch, M. Krause, M. Harz, J. Popp, K. Baumann, Gaussian mixture discriminant analysis for the single-cell differentiation of bacteria using micro-Raman spectroscopy, Chemom. Intell. Lab. Syst. 2009, 96, 159–171. DOI: 10.1016/j.chemolab.2009.01.008

  • S. G. Rohrer, K. Baumann, Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data, J. Chem. Inf. Model. 2009, 49, 169–184. DOI: 10.1021/ci8002649

  • S. Niedermeier, K. Singethan, S. G. Rohrer, M. Matz, M. Kossner, S. Diederich, A. Maisner, J. Schmitz, G. Hiltensperger, K. Baumann, U. Holzgrabe, J. Schneider-Schaulies, A Small-Molecule Inhibitor of Nipah Virus Envelope Protein-Mediated Membrane Fusion, J. Med. Chem. 2009, 52, 4257–4265. DOI: 10.1021/jm900411s

  • S. G. Rohrer, K. Baumann, Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics, J. Chem. Inf. Model. 2008, 48, 704–718. DOI: 10.1021/ci700099u

  • B. Degel, P. Staib, S. Rohrer, J. Scheiber, E. Martina, C. Büchold, K. Baumann, J. Morschhäuser, T. Schirmeister, Cis-Configured Aziridines Are New Pseudo-Irreversible Dual-Mode Inhibitors of Candida albicans Secreted Aspartic Protease 2, ChemMedChem 2008, 3, 302–315. DOI: 10.1002/cmdc.200700101

  • B. Waibel, J. Scheiber, C. Meier, M. Hammitzsch, K. Baumann, G. Scriba, U. Holzgrabe, Comparison of Cyclodextrin-Dipeptide Inclusion Complexes in the Absence and Presence of Urea by Means of Capillary Electrophoresis, Nuclear Magnetic Resonance and Molecular Modeling,
    Eur. J. Org. Chem. 2007, 18, 2921–2930. DOI: 10.1002/ejoc.200700052

  • U. Neugebauer, U. Schmid, K. Baumann, H. Simon, M. Schmitt, J. Popp, DNA tertiary structure and changes in DNA supercoiling upon interaction with ethidium bromide and gyrase monitored by UV resonance Raman spectroscopy, J. Raman Spectrosc. 2007, 38, 1246–1258. DOI: 10.1002/jrs.1760

  • U. Neugebauer, U. Schmid, K. Baumann, W. Ziebuhr, S. Kozitskaya, U. Holzgrabe, M. Schmitt, J. Popp, The Influence of Fluoroquinolone Drugs on the Bacterial Growth of S. epidermidis Utilizing the Unique Potential of Vibrational Spectroscopy, J. Phys. Chem. A 2007, 111, 2898–2906. DOI: 10.1021/jp0678397

  • U. Neugebauer, U. Schmid, K. Baumann, W. Ziebuhr, S. Kozitskaya, V. Deckert, M. Schmitt, J. Popp, Towards a Detailed Understanding of Bacterial Metabolism—Spectroscopic Characterization of Staphylococcus Epidermidis, ChemPhysChem. 2007, 8, 124–137. DOI: 10.1002/cphc.200600507

  • R. Vicik, M. Busemann, K. Baumann, T. Schirmeister, Inhibitors of Cysteine Proteases, Curr. Top. Med. Chem. 2006, 6, 331–353. DOI: 10.2174/156802606776287081

  • R. Vicik, M. Busemann, C. Gelhaus, N. Stiefl, J. Scheiber, W. Schmitz, F. Schulz, M. Mladenovic, B. Engels, M. Leippe, K. Baumann, T. Schirmeister, Aziridide-Based Inhibitors of Cathepsin L: Synthesis, Inhibition Activity, and Docking Studies, ChemMedChem 2006, 1, 1126–1141. DOI: 10.1002/cmdc.200600106

  • U. Neugebauer, U. Schmid, K. Baumann, U. Holzgrabe, W. Ziebuhr, S. Kozitskaya, W. Kiefer, M. Schmitt, J. Popp, Characterization of bacterial growth and the influence of antibiotics by means of UV resonance Raman spectroscopy, Biopolymers 2006, 82, 306–311. DOI: 10.1002/bip.20447

  • K. Gaus, P. Rösch, R. Petry, K.-D. Peschke, O. Ronneberger, H. Burkhardt, K. Baumann, J. Popp, Classification of lactic acid bacteria with UV-resonance Raman spectroscopy, Biopolymers 2006, 82, 286–290. DOI: 10.1002/bip.20448

  • N. Stiefl, I. Watson, K. Baumann, A. Zaliani, ErG:  2D Pharmacophore Descriptions for Scaffold Hopping, J. Chem. Inf. Model. 2006, 46, 208–220. DOI: 10.1021/ci050457y

  • C. Schmuck, M. Heil, J. Scheiber, K. Baumann, Charge Interactions Do the Job: A Combined Statistical and Combinatorial Approach to Finding Artificial Receptors for Binding Tetrapeptides in Water, Angew. Chem. Int. Ed. 2005, 44, 7208–7212. DOI: 10.1002/anie.200501812

  • U. Kaeppler, N. Stiefl, M. Schiller, B. Degel, R. Vicik, A. Breuning, W. Schmitz, K. Baumann, J. Ziebuhr, T. Schirmeister, A New Lead for Nonpeptidic Active-Site-Directed Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus Main Protease Discovered by a Combination of Screening and Docking Methods, J. Med. Chem. 2005, 48, 6832–6842. DOI: 10.1021/jm0501782

  • E. Martina, N. Stiefl, B. Degel, F. Schulz, A. Breuning, M. Schiller, R. Vicik, K. Baumann, J. Ziebuhr, T. Schirmeister, Screening of electrophilic compounds yields an aziridinyl peptide as new active-site directed SARS-CoV main protease inhibitor, Bioorg. Med. Chem. 2005, 15, 5365–5369. DOI: 10.1016/j.bmcl.2005.09.012

  • K. Baumann, Chance Correlation in Variable Subset Regression: Influence of the Objective Function, the Selection Mechanism, and Ensemble Averaging, QSAR Comb. Sci. 2005, 24, 1033–1046. DOI: 10.1002/qsar.200530134

  • N. Stiefl, K. Baumann, Structure-Based Validation of the 3D-QSAR Technique MaP, J. Chem. Inf. Model. 2005, 45, 739–749. DOI: 10.1021/ci049683i

  • C. Kahle, R. Deubner, C. Schollmayer, J. Scheiber, K. Baumann, U. Holzgrabe, NMR Spectroscopic and Molecular Modelling Studies on Cyclodextrin–Dipeptide Inclusion Complexes, Eur. J. Org. 2005, 2005, 1578–1589. DOI: 10.1002/ejoc.200400673

2000–2004

  • K. Baumann, N. Stiefl., Validation tools for variable subset selection, J. Comput.-Aided Mol. Design 2004, 18, 549–562. DOI: 10.1007/s10822-004-4071-5

  • D. P. Zlotos, D. Gündisch, S. Ferraro, C.M. Tilotta, N. Stiefl, K. Baumann, Bisquaternary caracurine V and iso-caracurine V salts as ligands for the muscle type of nicotinic acetylcholine receptors: SAR and QSAR studies, Bioorg. Med. Chem. 2004, 12, 6277–6285. DOI: 10.1016/j.bmc.2004.08.053

  • D. P. Zlotos, S. Buller, N. Stiefl, K. Baumann, K. Mohr, Probing the Pharmacophore for Allosteric Ligands of Muscarinic M2 Receptors:  SAR and QSAR Studies in a Series of Bisquaternary Salts of Caracurine V and Related Ring Systems, J. Med. Chem. 2004, 47, 3561–3571. DOI: 10.1021/jm0311341

  • V. Alptüzün, P. Kapková, K. Baumann, E. Erciyas, U. Holzgrabe, Synthesis and biological activity of pyridinium-type acetylcholinesterase inhibitors, J. Pharm. Pharmacol. 2003, 55, 1397–1404. DOI: 10.1211/0022357021855

  • N. Stiefl, G. Bringmann, C. Rummey, K. Baumann, Evaluation of extended parameter sets for the 3D-QSAR technique MaP: Implications for interpretability and model quality exemplified by antimalarially active naphthylisoquinoline alkaloids, J. Comput.-Aided Mol. Design 2003, 17, 347–365. DOI: 10.1023/A:1026125706388

  • P. Kapková, N. Stiefl, U. Sürig, B. Engels, K. Baumann, U. Holzgrabe, Synthesis, Biological Activity, and Docking Studies of New Acetylcholinesterase Inhibitors of the Bispyridinium Type, Arch. Pharm. Pharm. Med. Chem. 2003, 336, 523–540. DOI: 10.1002/ardp.200300795

  • N. Stiefl, K. Baumann, Mapping Property Distributions of Molecular Surfaces:  Algorithm and Evaluation of a Novel 3D Quantitative Structure−Activity Relationship Technique, J. Med. Chem. 2003, 46, 1390–1407. DOI: 10.1021/jm021077w

  • F. Wienen, S. Laug, K. Baumann, A. Schwab, S. Just, U. Holzgrabe, Determination of clotrimazole in mice plasma by capillary electrophoresis, J. Pharm. Biomed. Anal. 2002, 30, 1897–1887. DOI: 10.1016/S0731-7085(02)00531-9

  • K. Baumann, M. von Korff, H. Albert, A systematic evaluation of the benefits and hazards of variable selection in latent variable regression. Part II. Practical applications, J. Chemom. 2002, 16, 351–360. DOI: 10.1002/cem.729

  • K. Baumann, H. Albert, M. von Korff,  A systematic evaluation of the benefits and hazards of variable selection in latent variable regression. Part I. Theory and simulations, J. Chemom. 2002, 16, 339–350. DOI: 10.1002/cem.730

  • K. Baumann, An Alignment-Independent Versatile Structure Descriptor for QSAR and QSPR Based on the Distribution of Molecular Features,  J. Chem. Inf. Comput. Sci. 2002, 42, 26–35. DOI: 10.1021/ci990070t

  • U. Kuhl, M. von Korff, K. Baumann, C. Burschka, U. Holzgrabe, Stereochemical behaviour of κ-agonistic 2,4-dipyridin-2-yl-3,7-diazabicyclo[3.3.1]nonanones—influence of the substituent in position N3, J. Chem. Soc., Perkin Trans. 2001, 2, 2037–2042. DOI: 10.1039/B008648G

  • H. M. Botero Cid, C. Tränkle, K. Baumann, R. Pick, E. Mies-Klomfaß, E. Kostenis, K. Mohr, U. Holzgrabe, Structure−Activity Relationships in a Series of Bisquaternary Bisphthalimidine Derivatives Modulating the Muscarinic M2-Receptor Allosterically, J. Med. Chem. 2000, 43, 2155–2164. DOI: 10.1021/jm991136e

1995–1999

  • K. Baumann, Uniform-length molecular descriptors for Quantitative Structure-Property Relationships (QSPR), Quantitative Structure-Activity Relationships (QSAR), classification studies, and similarity searching. TrAC 1999, 18, 36–46. DOI: 10.1016/S0165-9936(98)00075-2

  • K. Baumann, Regression and calibration for analytical separation techniques. Part 2: Validation, weighted and robust regression. Process Control Qual. 1997, 10, 75–112.

  • K. Baumann, H. Wätzig, Regression and calibration for analytical separation techniques. Part 1: Design considerations, Process Control Qual. 1997, 10, 58–74.

  • K. Baumann, J. T. Clerc, Computer-assisted IR spectra prediction — linked similarity searches for structures and spectra, Anal. Chim. Acta 1997, 348, 327–343. DOI: 10.1016/S0003-2670(97)00238-9

  • C. Affolter, K. Baumann, J. T. Clerc, H. Schriber, E. Pretsch, Automatic Interpretation of Infrared Spectra, Mikrochim. Acta (Suppl.) 1997, 14, 143–147. DOI: 10.1007/978-3-7091-6840-0_17

  • K. Baumann, C. Affolter, E. Pretsch, J. T. Clerc, Numerical Structure Representation and IR Spectra Prediction, Mikrochim. Acta (Suppl.) 1997, 14, 275–276. DOI: 10.1007/978-3-7091-6840-0_56

  • K. Baumann, H. Wätzig, Appropriate calibration functions for capillary electrophoresis II. Heteroscedasticity and its consequences, J. Chromatogr. A 1995, 700, 9–20. DOI: 10.1016/0021-9673(95)00128-A

Editorials

  • K. Baumann, G. Schneider, Big Data and Deep Learning: A New Age of Molecular Informatics?, Mol. Inform. 2017, 36, 2. DOI: 10.1002/minf.201780132

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Molecular Informatis: From Models to Systems and beyond, Mol. Inform. 2016, 35, 2. DOI: 10.1002/minf.201680133

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Systems approaches and big data in molecular informatics, Mol. Inform. 2015, 34, 2. DOI: 10.1002/minf.201580131

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Molecular informatics going fully online, Mol. Inform. 2014, 33, 2. DOI: 10.1002/minf.201480131

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Sustained success of molecular informatics, Mol. Inform. 2013, 32, 3. DOI: 10.1002/minf.201380132

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Molecular informatics gaining impact, Mol. Inform. 2012, 31, 615. DOI: 10.1002/minf.201280931

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Molecular informatics - A leading discipline in a complex emerging field, Mol. Inform. 2012, 31, 3. DOI: 10.1002/minf.201290001

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Molecular informatics - The first year, Mol. Inform. 2011, 30,  3. DOI: 10.1002/minf.201190001

  • K. Baumann, G. F. Ecker, J. Mestres, G. Schneider, Molecular informatics - From models to molecules and systems, Mol. Inform. 2010, 29, 9. DOI: 10.1002/minf.201000271

  • K. Baumann, G. Schneider, From QSAR & Combinatorial Science to Molecular Informatics - Transition into the future and call for papers, QSAR Comb. Sci. 2009, 28, 623–624. DOI: 10.1002/qsar.200990023