Gisbert Schneider • Publications

List of Publications 1990-2009
Monographs:
1.
Schneider, G., Baringhaus, K. H. Molecular Design - Concepts and Applications. WileyVCH, Weinheim, 2008.
2.
Böhm, H.-J., Schneider, G. (Eds) Protein-Ligand Interaction – From Molecular
Recognition to Drug Design. Wiley-VCH, Weinheim, 2003.
3.
Schneider, G., So, S. S. Adaptive Systems In Drug Design. Landes Bioscience:
Georgetown, 2002.
4.
Böhm, H.-J., Schneider, G. (Eds) Virtual Screening for Bioactive Molecules. Wiley-VCH,
Weinheim, 2000.
5.
Wrede, P., Schneider, G. (Eds) Concepts in Protein Engineering and Design. Walter-deGruyter, Berlin, New York, 1994.
Special Journal Issues:
1.
Glen, R., Schneider, G. (Eds) Challenges in Virtual Screening. QSAR Comb. Sci. 2006,
25(12).
2.
Schneider, G., Downs, G. (Eds) Machine Learning Methods in QSAR Modeling. QSAR
Comb. Sci. 2003, 22(5).
Peer-reviewed Papers:
1.
Stauch, B., Hofmann, H., Perkovic, M., Weisel, M., Kopietz, F., Cichutek, K., Münk, C.,
Schneider, G. Model structure of APOBEC3C reveals a binding pocket modulating
ribonucleic acid interaction required for encapsidation. Proc. Natl. Acad. Sci. USA, 2009,
106, 12079-12084.
2.
Krüger, B., Weil, T., Schneider, G. Comparative virtual screening and novelty detection
for NMDA Glycine(B) antagonists. J. Comp. Aided Mol. Des., 2009, 23, 869-881.
3.
Esser, J., Rakonjac, M., Hofmann, B., Fischer, L., Provost, P., Schneider, G., Steinhilber,
D., Samuelsson, B., Rådmark, O. Coactosin-like protein functions as a stabilizing
chaperone for 5-lipoxygenase: role of tryptophan 102. Biochem. J., 2009, 425, 265-274.
4.
Sander, K., Kottke, T., Tanrikulu, Y., Proschak, E., Weitzel, L., Schneider, E. H., Seifert,
R., Schneider, G., Stark, H. 2,4-diaminopyrimidines as histamine H4 receptor ligands –scaffold optimization and pharmacological characterization. Bioorg. Med. Chem., 2009,17, 7186-7196.
5.
Hiss, J. A., Schneider, G. Domain organization of long autotransporter signal sequences.
Bioinform. Biol. Insights, 2009, 3, 189-204.
6.
Keppner, S., Proschak, E., Schneider, G., Spänkuch, U. Identification and validation of
a potent type II inhibitor of inactive polo-like kinase. ChemMedChem, 2009, 4, 18061809.
7.
Spork, S., Hiss, J., Sommer, M., Kooij, T. W. A., Chu, T., Schneider, G, Przyborski, J.
An unusual ERAD-like complex is targeted to the apicoplast of Plasmodium falciparum.
Eukaryot. Cell, 2009, 8, 1134-1145.
8.
Noeske, T., Trifanova, D., Kauss, V., Renner, S., Parsons, C. G., Schneider, G., Weil, T.
Synergism of virtual screening and medicinal chemistry: Identification and optimizationof allosteric antagonists of metabotropic glutamate receptor 1. Bioorg. Med. Chem.,
2009, 17, 5708-5715.
9.
Tausch, L., Siemoneit, U., Henkel, A., Poseckel, D., Kather, N., Franke, L., Hofmann, B.,
Schneider, G., Angioni, C., Geisslinger, G., Skarke, C., Holtmeier, W., Beckhaus, T.,
Karas, M., Jauch, J., Werz, O. Identification of human cathepsin G as a functional targetof boswellic acids from the anti-inflammatory remedy frankincense. J. Immunol., 2009,
183, 3433-3442.

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Feißt, C., Pergola, C., Rakonjac, M., Rossi, A., Koeberle, A., Dodt, G., Hoffmann, M.,
Hoernig, C., Fischer, L., Steinhilber, D., Franke, L., Schneider, G., Rådmark, O., Werz,
O. Hyperforin is a novel type of 5-lipoxygenase inhibitor with high efficacy in vivo. Cell.
Mol. Life Sci., 2009, 66, 2759-2771.
Koenig, M., Huenecke, S., Salzmann, E., Esser, R., Quaritsch, R., Steinhilber, D.,
Radeke, H. H., Martin, H., Bader, P., Klingebiel, T., Schwabe, D., Schneider, G.,
Lehrnbecher, T., Orth, A., Koehl, U. Multivariate analyses of immune reconstitution inchildren following allogenic stem cell transplantation: Risk-estimation based on agematched leukocyte subpopulation. Bone Marrow Transpl., 2009, 45, 613-621.
Rupp, M., Schneider, P., Schneider, G. Distance phenomena in high-dimensional
chemical descriptor spaces: consequences for similarity-based approaches. J. Comp.
Chem., 2009, 30, 2285-2296.
Löwer, M., Schneider, G. Prediction of type III secretion signals in genomes of Gramnegative bacteria. PLoS ONE, 2009, 4, 35917.
Hiss, J. A., Schneider, G. Architecture, function and prediction of long signal peptides.
Brief. Bioinform., 2009, 10, 569-578.
Zettl, H., Dittrich, M., Steri, R., Proschak, E., Rau, O., Steinhilber, D., Schneider, G.,
Lämmerhofer, M., Schubert-Zsilavecz, M. Novel pirinixic acids as PPARα preferential
dual PPARα/γ agonists. QSAR Comb. Sci., 2009, 28, 576-586.
Tanrikulu, Y., Proschak, E., Werner, T., Geppert, T., Todoroff, N., Klenner, A., Kottke,T., Sander, K., Schneider, E., Seifert, R., Stark, H., Clark, T., Schneider, G. Homologymodel adjustment and ligand screening with a pseudoreceptor of the human histamine
H4 receptor. ChemMedChem, 2009, 4, 820-827.
Koeberle, A., Siemoneit, U., Northoff, H., Hofmann, B., Schneider, G., Werz, O. MK-886,
an inhibitor of the 5-lipoxygenase-activating protein, inhibits cyclooxygenase-1 activity
and suppresses platelet aggregation. Eur. J. Pharmacol., 2009, 608, 84-90.
Krüger, B., Dietrich, A., Baringhaus, K.-H., Schneider, G. Scaffold-hopping potential offragment-based de novo design: The chances and limits of variation. Comb. Chem. HighThroughput Screen., 2009, 12, 383-396.
Schneider, G., Tanrikulu, Y., Schneider, P. Self-organizing molecular fingerprints: aligand-based view on druglike chemical space and off-target prediction. Future Med.
Chem., 2009, 1, 213-218.
Perković, M., Schmidt, S., Marino, D., Russell, R. A., Stauch, B., Hofmann, H., Kopietz,
F., Kloke, B.-P., Zielonka, J., Ströver, H., Hermle, J., Lindemann, D., Pathak, V. K.,
Schneider, G., Löchelt, M., Cichutek, K., Münk, C. Species-specific inhibition of
APOBEC3C by the prototype foamy virus protein Bet. J. Biol. Chem., 2009, 284, 58195826.
Reisen, F., Schneider, G., Proschak, E. ReactionMQL: Line notation for the
representation of chemical reactions. J. Chem. Inf. Model., 2009, 49, 6-12.
Hähnke, V., Hofmann, B., Grgat, T., Proschak, E., Steinhilber, D., Schneider, G. PhAST:
Pharmacophore Alignment Search Tool. J. Comput. Chem., 2009, 30, 761-771.
Schneider, P., Tanrikulu, Y., Schneider, G. Self-organizing maps in drug discovery:
Library design, scaffold-hopping, repurposing. Curr. Med. Chem., 2009, 16, 258-266.
Weisel, M., Proschak, E., Kriegl, J. M., Schneider, G. Form follows function: Shapeanalysis of protein cavities for receptor-based drug design. Proteomics, 2009, 9, 451459.
Schneider, G., Hartenfeller, M., Reutlinger, M., Tanrikulu, Y., Proschak, E., Schneider,P. Voyages to the (un)known: Adaptive design of bioactive compounds. Trends
Biotechnol., 2009, 27, 18-26.
Altmann, K.-H., Buchner, J., Kessler, H., Diederich, F., Kräutler, B., Lippard, S., Liskamp,
R., Müller, K., Samori, B., Schneider, G., Schwalbe, H., Toniolo, C., van Boeckel, C. A.
A., Waldmann, H., Walsh, C. T., Nolan, E. M. The state of the art in chemical biology.
ChemBioChem, 2009, 10, 16-29.

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Proschak, E., Zettl, H., Tanrikulu, Y., Weisel, M., Kriegl, J. M., Rau, O., SchubertZsilavecz, M., Schneider, G. From molecular shape to potent bioactive agents I:
Bioisosteric replacement of molecular fragments. ChemMedChem, 2009, 4, 41-44.
Proschak, E., Sander, K., Zettl, H., Tanrikulu, Y., Rau, O., Schneider, P., SchubertZsilavecz, M., Stark, H., Schneider, G. From molecular shape to potent bioactive agents
II: Fragment-based de novo design. ChemMedChem, 2009, 4, 45-48.
Tanrikulu, Y., Rau, O., Schwarz, O., Proschak, E., Siems, K., Müller-Kuhrt, L., SchubertZsilavecz, M., Schneider, G. Structure-based pharmacophore screening for natural
product-derived PPARγ agonists. ChemBioChem, 2009, 10, 75-78.
Meissner, M., Koch, O., Klebe, G., Schneider, G. Prediction of turns types in protein
structure by machine-learning classifiers. Proteins, 2008, 74, 344-352.
Hofmann, B., Franke, L., Proschak, E., Tanrikulu, Y., Schneider, P., Steinhilber, D.,
Schneider, G. Scaffold-hopping cascade yields potent inhibitors of 5-lipoxygenase.
ChemMedChem, 2008, 3, 1535-1538.
Löwer, M., Weydig, C., Metzler, D., Reuter, A., Starzinski-Powitz, A., Wessler, S.,
Schneider, G. Prediction of extracellular proteases of the human pathogen Helicobacter
pylori reveals proteolytic activity of the Hp1018/19 protein HtrA. PLoS ONE, 2008, 3,
e3510.
Grabowski, K., Baringhaus, K.-H., Schneider, G. Scaffold diversity of natural-products:
Inspiration for combinatorial library design. Nat. Prod. Rep., 2008, 25, 892-904.
Alig, L., Alsenz, J., Andjelkovic, M., Bendels, S., Bénardeau, A., Bleicher, K., Bourson,
A., David-Pierson, P., Guba, W., Hildbrand, S., Kube, D., Lübbers, T., Mayweg, A. V.,
Narquizian, R., Neidhart, W., Nettekoven, M., Plancher, J. M., Rocha, C., Rogers-Evans,
M., Röver, S., Schneider, G., Taylor, S., Waldmeier, P. Benzodioxoles: Novelcannabinoid-1 receptor inverse agonists for the treatment of obesity. J. Med. Chem.,
2008, 51, 2115-2127.
Schüller, A., Schneider, G. Identification of hits and lead structure candidates with limited
resources by adaptive optimization. J. Chem. Inf. Model., 2008, 48, 1473-1491.
Tanrikulu, Y., Schneider, G. Pseudoreceptor models in drug design: Bridging ligand- andreceptor-based virtual screening. Nat. Rev. Drug Discov., 2008, 7, 668-677.
Hiss, J., Resch, E., Schreiner, A., Meissner, M., Starzinski-Powitz, A., Schneider, G.
Domain organization of long signal peptides of single-pass integral membrane proteins
reveals multiple functional capacity. PLoS ONE, 2008, 3, e2767.
Resch, E., Quaiser, S., Quaiser, T., Schneider, G., Starzinski-Powitz, A., Schreiner, A.
Synergism of shrew-1’s signal peptide and transmembrane segment required for plasma
membrane localization. Traffic, 2008, 9, 1344-1353.
Hartenfeller, M., Proschak, E., Schüller, A., Schneider, G. Concept of combinatorial denovo design of druglike molecules by particle swarm optimization. Chem. Biol. DrugDes., 2008, 72, 16-26.
Hiss, J. A., Przyborski, J. M., Schwarte, F. Lingelbach, K., Schneider, G. The
Plasmodium export element revisited. PLoS ONE, 2008, 3, e1560.
Schüller, A., Suhartono, M., Fechner, U., Tanrikulu, Y., Breitung, S., Scheffer, U., Göbel,M. W., Schneider, G. The concept of template-based de novo design from drug-derived
molecular fragments and its application to TAR RNA. J. Comp. Aided Mol. Des., 2008,
22, 59-68.
Grabowski, K., Proschak, E., Baringhaus, K.-H., Rau, O., Schubert-Zsilavecz, M.,
Schneider, G. Bioisosteric replacement of molecular scaffolds: From natural products tosynthetic compounds. Nat. Prod. Commun., 2008, 3, 1355-1360.
Schmuker, M., Schneider, G. Processing and classification of chemical data inspired by
insect olfaction. Proc. Natl. Acad. Sci. USA, 2007, 104, 20285-20289.
Renner, S., Hechenberger, M., Noeske, T., Böcker, A., Jatzke, C., Schmuker, M.,
Parsons, C. G., Weil, T., Schneider, G. Searching for drug scaffolds with 3D
pharmacophores and neural network ensembles. Angew. Chem. Int. Ed., 2007, 46,5336-5339.
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Franke, L., Schwarz, O., Müller-Kuhrt, L., Hoernig, C., Fischer, L., George, S., Tanrikulu,
Y., Schneider, P., Werz, O., Steinhilber, D., Schneider, G. Identification of natural
product-derived inhibitors of 5-lipoxygenase activity by ligand-based virtual screening. J.
Med. Chem., 2007, 50, 2640-2646.
Proschak, E., Rupp, M., Derksen, S., Schneider, G. Shapelets: Possibilities andlimitations of shape-based virtual screening. J. Comp. Chem., 2007, 29, 108-114.
Tanrikulu, Y. Nietert, M., Scheffer, U., Proschak, E., Grabowski, K., Schneider, P.,
Weidlich, M., Karas, M., Göbel, M, Schneider, G. Scaffold-hopping by “fuzzy”
pharmacophores and application to RNA targets. ChemBioChem, 2007, 8, 1932-1936.
Noeske, T., Jirgensons, A., Stachenkovs, I., Renner, S., Jaunzeme, I., Trifanova, D.,
Hechenberger, M., Bauer, T., Schneider, G., Parsons, C. G., Weil, T. Virtual screening
for selective allosteric mGluR1 antagonists and structure-activity relationshipinvestigations for coumarine derivatives. ChemMedChem, 2007, 2, 1763-1773.
Böcker, A., Sasse, B. C., Nietert, M., Stark, H., Schneider, G. GPCR-targeted library
design: Novel dopamine D3 receptor antagonists. ChemMedChem, 2007, 2, 1000-1005.
Werz, O., Fischer, L., Hornig, M., Pergola, C., Meindl, N., Franke, L., Tarikulu, Y., Dodt,
G., Schneider, G., Steinhilber, D. On the molecular mechanism of 5-lipoxygenase
product synthesis inhibition by licofelone. Brit. J. Pharmacol., 2007, 152, 471-480.
Siemoneit, U., Hofmann, B., Kather, N., Lamkemeyer, T., Madlung, J., Franke, L.,
Schneider, G., Jauch, J., Poeckel, D., Werz, O. Identification and functional analysis of
cyclooxygenase-1 as a molecular target of boswellic acids. Biochem. Pharmacol., 2007,
75, 503-513.
Givehchi, A., Ludwig, V., Boden, O., Krebs, A., Scheffer, U., Göbel, M., Schneider, G.
Classification and prediction of tripeptides inhibiting HIV-1 Tat/TAR-RNA interaction
using a self-organizing map. Lett. Drug Des. Discov., 2007, 4, 410-416.
Byvatov, E., Baringhaus, K.-H., Schneider, G., Matter, H. Virtual screening filter for
identification of cytochrome P450 2C9 (CYP2C9) inhibitors. QSAR Comb. Sci., 2007,
26, 618-628.
Meissner, M., Schneider, G. Protein folding simulation by particle swarm optimization.
Open Struct. Biol. J., 2007, 1, 1-6.
Schmuker, M., Schwarte, F., Brück, A., Proschak, E., Tanrikulu, Y., Givehchi, A.,
Scheiffele, K., Schneider, G. SOMMER: Self-organizing maps for education andresearch. J. Mol. Model., 2007, 13, 225-228.
Grabowski, K., Schneider, G. Properties and architecture of drugs and natural products
revisited. Curr. Chem. Biol., 2007, 1, 115-127.
Rabal, O., Schneider, G., Borrell, J. I., Teixidó, J. Structure-based virtual screening of
FGFR inhibitors: Cross-decoys and induced-fit effect. Biodrugs, 2007, 21, 31-45.
Schmuker, M., de Bruyne, M., Hähnel, M., Schneider, G. Predicting olfactory receptor
neuron responses from odorant structure. Chemistry Central J., 2007, 1, 11.
Weisel, M., Proschak, E., Schneider, G. PocketPicker: Analysis of ligand binding-sites
with shape descriptors. Chemistry Central J., 2007, 1, 7.
Rupp, M., Proschak, E., Schneider, G. Kernel approach to molecular similarity based on
iterative graph similarity. J. Chem. Inf. Model., 2007, 47, 2280-2286.
Proschak, E., Wegner, J., Schüller, A., Schneider, G., Fechner, U. Molecular Query
Language (MQL): A context-free grammar for substructure matching. J. Chem. Inf.
Model., 2007, 47, 295-301.
Schüller, A., Hähnke, V., Schneider, G. SmiLib v2.0: A Java-based tool for rapid
combinatorial library enumeration. QSAR Comb. Sci., 2007, 26, 407-410.
Hiß, J., Bredenbeck, A., Losch, F. O., Wrede, P., Walden, P., Schneider, G. Design of
MHC I stabilizing peptides by agent-based exploration of sequence space. Prot. Eng.
Des. Sel., 2007, 20, 99-108.

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Fechner, U., Schneider, G. Flux (2): Comparison of molecular mutation and crossover
operators for ligand-based de novo design. J. Chem. Inf. Model., 2007, 47, 656-667.
Fechner, U., Schneider, G. Flux (1): A virtual synthesis scheme for fragment-based denovo design. J. Chem. Inf. Model., 2006, 46, 699-707.
Meissner, M., Schmuker, M., Schneider, G. Optimized Particle Swarm Optimization(OPSO) and its application to artificial neural network training. BMC Bioinformatics,
2006, 7, 125-136.
Renner, S., Schneider, G. Scaffold-hopping potential of ligand-based similarity concepts.
ChemMedChem, 2006, 1, 181-185.
Noeske, T., Sasse, B. C., Stark, H., Parsons, C. G., Weil, T., Schneider, G. Predicting
compound selectivity by self-organizing maps: cross-activities of metabotropic glutamate
receptor antagonists. ChemMedChem, 2006, 1, 1066-1068.
Derksen, S., Rau, O., Schneider, P., Schubert-Zsilavecz, M., Schneider, G. Virtual
screening for PPAR modulators using a probabilistic neural network. ChemMedChem,
2006, 1, 1346-1350.
Schüller, A., Fechner, U., Renner, S., Franke, L., Weber, L., Schneider, G. A pseudoligand approach to virtual screening. Comb. Chem. High-Throughput Screen., 2006, 9,359-364.
Böcker, A., Schneider, G., Teckentrup, A. NIPALSTREE: A new hierarchical clustering
approach for large compound libraries and its application to virtual screening. J. Chem.
Inf. Model., 2006, 46, 2220-2229.
Renner, S., Schwab, C., Gasteiger, J., Schneider, G. Impact of conformational flexibilityon three-dimensional similarity searching. J. Chem. Inf. Model., 2006, 46, 2324-2332.
Schneider, G., Schneider, P., Renner, S. Scaffold-hopping: How far can you jump?
QSAR Comb. Sci., 2006, 25, 1162-1171.
Schneider, G, Fechner, U. Computer-based de novo design of druglike molecules. Nat.
Rev. Drug Discov., 2005, 4, 649-663.
Werz, O., Tretiakova, I., Michel, A., Ulke, A., Hörnig, M., Franke, L., Schneider, G.,
Samuelsson, B., Rådmark, O., Steinhilber, D. Caspase-mediated degradation of human
5-lipoxygenase in B-lymphocytic cells. Proc. Natl. Acad. Sci. USA, 2005, 102, 1316413169.
Renner, S., Noeske, T., Parsons, C. P., Weil, T., Schneider, G. New allosteric modulatorsof metabotrobic glutamate receptor 5 (mGluR5) found by ligand-based virtual screening.
ChemBioChem, 2005, 6, 620-625.
Byvatov, E., Sasse, B. C., Stark, H., Schneider, G. From virtual to real screening for
novel D3 dopamine receptor ligands. ChemBioChem, 2005, 6, 997-999.
Renner, S., Ludwig, V., Boden, O., Scheffer, U., Göbel, M., Schneider, G. New inhibitorsof the Tat-TAR RNA interaction found with a “fuzzy” pharmacophore model.
ChemBioChem, 2005, 6, 1119-1125.
Paetz, J., Schneider, G. A neuro-fuzzy approach to virtual screening in molecularbioinformatics. Fuzzy Sets Syst., 2005, 152, 67-82.
Böcker, A., Derksen, S., Schmidt, E., Teckentrup, A., Schneider, G. A hierarchicalclustering approach for large compound libraries. J. Chem. Inf. Model., 2005, 45, 807815.
Fechner, U., Paetz, J., Schneider, G. Comparison of three holographic fingerprint
descriptors and their binary counterparts. QSAR Comb. Sci., 2005, 24, 961-967.
Franke, L., Byvatov, E., Werz, O., Steinhilber, D., Schneider, P., Schneider, G. Extraction
and visualization of potential pharmacophore points using Support Vector Machines:
Application to ligand-based virtual screening for COX-2 inhibitors. J. Med. Chem., 2005,
48, 6997-7004.
Givehchi, A., Schneider, G. Multi-space classification for predicting GPCR ligands. Mol.
Divers., 2005, 9, 371-383.
Fechner, U., Schneider, G. Optimization of a pharmacophore-based correlation vector
descriptor. QSAR Comb. Sci., 2004, 23, 19-22.
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Fechner, U., Schneider, G. Evaluation of distance metrics for ligand-based similarity
searching. ChemBioChem, 2004, 5, 538-540.
86. Byvatov, E., Schneider, G. SVM-based feature selection for characterization of focusedcompound collections. J. Chem. Inf. Comput. Sci., 2004, 44, 993-999.
87. Schneider, G., Fechner, U. Advances in the prediction of protein targeting signals.
Proteomics, 2004, 4, 1571-1580.
88. Boecker, A., Schneider, G., Teckentrup, A. Current status of HTS data mining
approaches. QSAR Comb. Sci., 2004, 23, 207-213.
89. Givehchi, A., Schneider, G. Impact of descriptor vector scaling on the classification ofdrugs and nondrugs with artificial neural networks. J. Mol. Model., 2004, 10, 204-211.
90. Rogers-Evans, M., Alanine, A. I., Bleicher, K. H., Kube, D., Schneider, G. Identificationof novel cannabinoid receptor ligands via evolutionary de novo design and rapid parallel
synthesis. QSAR Comb. Sci., 2004, 23, 426-430.
91. Renner, S., Schneider, G. Fuzzy pharmacophore models from molecular alignments forcorrelation-vector based virtual screening. J. Med. Chem., 2004, 47, 4653-4664.
92. Schmuker, M., Givehchi, A., Schneider, G. Impact of different software implementations
on the performance of the Maxmin method for diverse subset collection. Mol. Divers.,
2004, 8, 421-425.
93. Martin, O., Brandriss, M. C., Schneider, G., Bakalinsky, A. T. Improved anaerobic use ofarginine by S.cerevisiae. Appl. Env. Microbiol., 2003, 69, 1623-1628.
94. Schneider, G, Nettekoven, M. Ligand-based combinatorial design of selective purinergic
receptor (A2A) antagonists using self-organizing maps. J. Comb. Chem., 2003, 5, 233237.
95. Givehchi, A., Dietrich, A., Wrede, P., Schneider, G. ChemSpaceShuttle: A tool for data
mining in drug discovery by classification, projection, and 3D visualization. QSAR Comb.
Sci., 2003, 5, 549-559.
96. Byvatov, E., Schneider, G. Applications of support vector machines in bioinformatics.
Appl. Bioinf., 2003, 2, 67-77.
97. Schüller, A., Schneider, G., Byvatov, E. SMILIB: Rapid assembly of combinatorial
libraries in SMILES notation. QSAR Comb. Sci., 2003, 22, 719-721.
98. Bender, A., van Dooren, G., Ralph, S., McFadden, G. I., Schneider, G. Properties andprediction of mitochondrial transit peptides from Plasmodium falciparum. Mol. Biochem.
Parasitol., 2003, 132, 59-66.
99. Schneider, P, Schneider, G. Collection of bioactive reference compounds for focused
library design. QSAR Comb. Sci., 2003, 22, 713-718.
100. Byvatov, E., Fechner, U., Sadowski, J., Schneider, G. Comparison of support vector
machines and artificial neural networks for drug-likeness prediction. J. Chem. Inf.
Comput. Sci., 2003, 43, 1882-1889.
101. Fechner, U., Franke, L., Renner, S., Schneider, P., Schneider, G. Comparison ofcorrelation vector methods for ligand-based similarity searching. J. Comput. Aided Mol.
Des., 2003, 17, 687-698.
102. Schneider, G., Böhm, H. J. Virtual screening and fast automated docking methods. Drug
Discov. Today, 2002, 7, 64-70.
103. Roche, O., Schneider, P., Zuegge, J., Guba, W., Kansy, M., Alanine, A., Bleicher, K.,
Danel, F., Gutknecht, E. M., Rogers- Evans, M., Neidhart, W., Stalder, H., Dillon, M.,
Sjøgren, E., Fotouhi, N., Gillespie, P., Goodnow, R., Harris, W., Jones, P., Taniguchi,M., Tsujii, S., von der Saal, W., Zimmermann, G., Schneider, G. Development of a virtual
screening method for identification of "frequent hitters" in compound libraries. J. Med.
Chem., 2002, 45, 137-142.
104. Roche, O., Trube, G., Zuegge, J., Pflimlin, P., Alanine, A., Schneider, G. A virtual
screening method for prediction of the hERG potassium channel liability of compound
libraries. ChemBioChem, 2002, 3, 455-459.

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105. Zuegge, J., Fechner, U., Roche, O., Parrott, N. J., Engkvist, O., Schneider, G. A fast
virtual screening filter for cytochrome P450 3A4 inhibition liability of compound libraries.
Quant. Struct. Act. Relat., 2002, 21, 249-256.
106. Schneider, G. Trends in virtual combinatorial library design. Curr. Med. Chem., 2002, 9,2095-2101.
107. Schneider, G., Neidhart, W., Adam, G. Integrating virtual screening to the quest for novel
membrane protein ligands. Curr. Med. Chem. Cent. Nerv. Syst. Agents, 2001, 1, 99-112.
108. Emanuelsson, O., von Heijne, G., Schneider, G. Analysis and prediction of mitochondrial
targeting sequences. Methods Cell Biol., 2001, 65, 175-187.
109. Zuegge, J., Ebeling, M., Schneider, G. H-BloX – Visualizing alignment block entropies.
J. Mol. Graph. Model., 2001, 19, 304-306.
110. Lee, M. L., Schneider, G. Scaffold architecture and pharmacophoric properties of tradedrugs and natural products. J. Comb. Chem., 2001, 3, 284-289.
111. Zuegge, J., Schneider, G., Coassolo, P., Lavé, T. Prediction of hepatic metabolic
clearance – comparison and assessment of prediction models. Clin. Pharmacokinet.,
2001, 40, 553-563.
112. Zuegge, J., Ralph, S., Schmuker, M., McFadden, G. I., Schneider, G. Deciphering
apicoplast targeting signals - feature extraction from nuclear-encoded precursors of
Plasmodium falciparum apicoplast proteins. Gene, 2001, 280, 19-26.
113. Schneider, G., Chomienne-Clement, O., Hilfiger, L., Kirsch, S., Böhm, H.J., Schneider,
P., Neidhart, W. Virtual screening for bioactive molecules by evolutionary de novo
design. Angew. Chemie Int. Ed., 2000, 39, 4130-4133.
114. Schneider, G. Neural networks are useful tools for drug design. Neural Networks, 2000,
13, 15-16.
115. Stahl, M., Taroni-Osterroth, C., Schneider, G. (2000) Mapping of protein surface cavities
and prediction of enzyme class by a self-organizing neural network. Protein Eng., 2000,
13, 83-88.
116. Schneider, G., Lee, M.-L., Stahl, M., Schneider, P. De novo design of moleculararchitectures by evolutionary assembly of drug-derived building blocks. J. Comput. Aided
Mol. Des., 2000, 14, 487-494.
117. Schneider, G., Neidhart, W., Giller, T., Schmid, G. “Scaffold-Hopping” by topologicalpharmacophore search: A contribution to virtual screening. Angew. Chemie Int. Ed.,
1999, 38, 2894-2896.
118. Schneider, G., Coassolo, P., Lavé, T. Combining in vitro and in vivo pharmacokinetic
data for prediction of hepatic drug clearance in humans by artificial neural networks andmultivariate statistical techniques. J. Med. Chem., 1999, 42, 5072- 5076.
119. Schneider, G. How many potentially secreted proteins are contained in a bacterial
genome? Gene, 1999, 237, 113-121; Gene, 1999, 240, 245.
120. Stahl, M., Bur, D., Schneider, G. Mapping of proteinase active sites projection of surfacederived correlation vectors. J. Comput. Chem., 1999, 20, 336-347.
121. Schneider, G., Sjöling, S., Wallin, E., Wrede, P., Glaser, E., von Heijne, G. Feature
extraction from endopeptidase cleavage sites in mitochondrial targeting peptides.
Proteins, 1998, 30, 49-60.
122. Wrede, P., Landt, O., Klages, S., Fatemi, A., Hahn, U., Schneider, G. Peptide design
aided by neural networks: biological activity of artificial signal peptidase I cleavage sites.
Biochemistry, 1998, 37, 3588-3593.
123. Schneider, G., Wrede, P. Artificial neural networks for computer-based molecular design.
Prog. Biophys. Mol. Biol., 1998, 70, 175-222.
124. Schneider, G., Schrödl, W., Wallukat, G., Nissen, E., Rönspeck, G., Müller, J., Wrede,P., Kunze, R. Peptide design by artificial neural networks and computer-based
evolutionary search. Proc. Natl. Acad. Sci. USA, 1998, 95, 12179-12184.
125. Schneider, G., Schneider, P., Wrede, P. An approach to forward and inverted protein
folding by empirical property profiles and evolutionary algorithms. Min. Invas. Med.,
1997, 8, 42- 53.
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Gisbert Schneider • Publications
126. Lohmann, R., Schneider, G., Wrede, P. Structure optimization of an artificial neural filter
detecting membrane- spanning amino acid sequences. Biopolymers, 1996, 38, 13-29.
127. Schneider, G., Schuchhardt, J., Wrede, P. Evolutionary optimization in multimodal
search space. Biol. Cybern., 1996, 74, 203-207.
128. Jagla, B., Schneider, G., Schuchhardt, J., Wrede, P. Vorhersage der cis/transKonformation von Peptidgruppen in Proteinen aus der Aminosäuresequenz. Min. Invas.
Med., 1996, 7, 2- 11.
129. Wrede, P., Schneider, G., Schuchhardt, J., Müller, G. Analysis of amino acid sequenceswith artificial neuronal networks. Chemie in Unserer Zeit, 1996, 30, 172-181.
130. Wrede, P., Schneider, G., Schuchhardt, J., Müller, S., Müller, G. Bioinformation methods
for peptide design. Biospekrum, 1996, 18, 21-23.
131. Schneider, G., von Heijne G., Wrede, P. Model of mitochondrial precursor processing by
signal peptidases. Min. Invas. Med., 1996, 7, 127-130.
132. Schuchhardt, J., Schneider, G., Reichelt J., Schomburg, D., Wrede, P. (1996) Local
structural motifs of protein backbones are classified by self-organizing neural networks.
Protein Eng., 1996, 9, 833-842.
133. Schneider, G., Schuchhardt, J., Hobohm, U., Jagla, B., Wrede, P. Classification of local
protein backbone motifs by Kohonen networks. Min. Invas. Med., 1996, 7, 164-168.
134. Schneider, G., Schuchhardt, J., Wrede, P. Peptide design in machina: development ofartificial mitochondrial protein precursor cleavage-sites by simulated molecular evolution.
Biophys. J., 1995, 68, 434-447.
135. Schneider, G., Hahn, U., Fatemi, A., Müller, G., Wrede, P. Peptide design in machina:
Artificial signal peptidase cleavage-sites are processed in vivo. Min. Invas. Med., 1995,
6, 72-77.
136. Schneider, G., Schuchhardt, J., Wrede, P. Simulated molecular evolution and artificial
neural networks for sequence-oriented protein design: An evaluation. Endocytobiosis
Cell Res., 1995, 11, 1-18.
137. Schneider, G., Schuchhardt, J., Wrede, P. Development of simple fitness landscapes for
peptides by artificial neural filter systems. Biol. Cybern., 1995, 73, 245-254.
138. Schneider, G., Grunert H.P., Schuchhardt, J., Wolf, K., Zeichhardt, H., Habermehl, K.H.,
Müller, G., Wrede, P. A peptide selection scheme for systematic evolutionary design andconstruction of synthetic peptide libraries. Min. Invas. Med., 1995, 6, 106-115.
139. Schneider, G., Grammel, O., Todt, T., Wrede, P. Patterns of amino acid properties
around mitochondrial signal peptidase I cleavage-sites. Protein Peptide Lett., 1995, 2,
327-332.
140. Schneider, G., Wrede, P. The rational design of amino acid sequences by artificial neuralnetworks and simulated molecular evolution: De novo design of an idealized leader
peptidase cleavage-site. Biophys. J., 1994, 66, 335-344.
141. Schneider, G., Wrede, P. Optimizing amino acid sequences by simulated molecular
evolution. Mathem. Res., 1994, 81, 335-346.
142. Schneider, G., Wrede, P. Sequence analysis of Intercellular Adhesion Molecule-1(ICAM-1) by artificial neural networks: identification of a signal peptide and a membranespanning region. Min. Invas. Med., 1994, 5, 137-141.
143. Schneider, G., Todt, T., Wrede, P. De novo design of proteins and peptides: machinegenerated sequences by the PROSA program. Computer Applic. Biosci., 1994, 10, 7577.
144. Schneider, G., Schuchhardt, J., Wrede, P. Artificial neural networks and simulated
molecular evolution are potential tools for sequence-oriented protein design. Computer
Applic. Biosci., 1994, 10, 635-645.
145. Lohmann, R., Schneider, G., Behrens, D., Wrede, P. A neural network model predicting
membrane-spanning amino acid sequences. Protein Sci., 1994, 3, 1597-1601.
146. Schneider, G., Wrede, P. PROFI - a tool for the analysis of protein sequence featuresusing a simple artificial neural network. Protein Seq. Data Anal., 1993, 5, 419-421.

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Gisbert Schneider • Publications
147. Schneider, G., Wrede, P. Development of artificial neural filters for pattern recognition inprotein sequences. J. Mol. Evol., 1993, 36, 586-595.
148. Schneider, G., Wrede, P. Vorhersage der Sekundärstruktur von Proteinen aus derAminosäuresequenz mit künstlichen neuronalen Netzen. Angew. Chemie, 1993, 105,
1192-1194.
149. Schneider, G., Röhlk, S., Wrede, P. Analysis of signal peptidase cleavage-sites with a
Perceptron-type neural network. Biochem. Biophys. Res. Comm., 1993, 194, 951-959.
150. Schneider, G., Wrede, P. Modular feature extraction in amino acid sequences by artificial
neural networks: Analog model for symbiogenous constraints. Endocytobiosis Cell Res.,
1992, 9, 1-12.
151. Schneider, G., Christmann, H., Wrede, P. Protein targeting in the view ofEndocytobiology. Endocytobiosis Cell Res., 1992, 9, 83-101.
152. Schneider, G., Wrede, P., Hoffmann, A. Protein targeting and translocation: A teachingapproach. Endocytobiosis Cell Res., 1991, 8, 93-108.
153. Schneider, G. Contributions to the knowledge of Neofulla (Plecoptera) from Chile andArgentina. Studies Neotrop. Fauna Env., 1990, 25, 249-251.
Chapters in Collective Volumes:
1.
Schneider, G., Hartenfeller, M., Proschak, E. De novo drug design. In: Modern
Approaches to Lead Discovery (Z. Rankovic, R. Morphy; Eds). Wiley & Sons, New York,2009, pp. 165-186.
2.
Schneider, G., Schüller, A. Adaptive combinatorial design of focused compound libraries.
In: Ligand-Macromolecule Interactions in Drug Discovery (A.C. Roque, Ed.). Humana
Press, Totowa, 2009, pp. 135-147.
3.
Schneider, G., Schneider, P. ‘Promiscuous’ ligands and targets provide opportunities for
drug design. In: Systems Chemistry (C. Kettner, M. Hicks; Eds). Logos, Berlin, 2008, pp.
249-260.
4.
Proschak, E., Tanrikulu, Y., Schneider, G. Fragment-based de novo design of druglikecompounds. In: Chemoinformatics Approaches to Virtual Screening (A. Varnek, A.
Tropsha; Eds). RSC Publishing, Cambridge, 2008, pp. 217-239.
5.
Schneider, G., Proschak, E., Grabowski, K., Schneider, P., Tanrikulu, Y. More thancolored blobs – ‘Fuzzy’ descriptions of potential pharmacophore points. In: MolecularInteractions – Bringing Chemistry to Life (C. Kettner, M. Hicks; Eds). Logos, Berlin, 2007,
pp. 173-184.
6.
Bleicher, K. H., Alanine, A. I., Roger-Evans, M., Schneider, G. GPCR hit discovery
beyond HTS. In: The Chemical Theatre of Biological Systems (C. Kettner, M. Hicks;
Eds). Logos, Berlin, 2005, pp. 133-146.
7.
Schneider, G., Renner, S., Fechner, U. Navigation in chemical space based oncorrelation-vector representations of molecules. In: The Chemical Theatre of Biological
Systems (C. Kettner, M. Hicks; Eds). Logos, Berlin, 2005, pp. 197-218.
8.
Renner, S., Fechner, U., Schneider, G. Alignment-free pharmacophore patterns – A
correlation-vector approach. In: Pharmacophores and Pharmacophore Searches (T.
Langer, T. Hoffmann; Eds). Wiley-VCH, Weinheim, 2005, pp. 49-79.
9.
Schneider, G., Schneider, P. Navigation in chemical space: Ligand-based design offocused compound libraries. In: Chemogenomics in Drug Discovery (H. Kubinyi, G.
Müller; Eds). Wiley-VCH, Weinheim, 2004, pp. 341-376.
10. Paetz, J., Fechner, U., Franke, L., Renner, S., Schneider, P., Schneider, G.
Pharmacophore feature selection with a neuro-fuzzy system. In: Proceedings of the 4th
Europ. Symp. on Intelligent Technologies, Hybrid Systems and their Implementation on
Smart Adaptive Systems (EUNITE 2004), (Ed. Elite-Foundation). Aachen, Mainz
Wissenschaftsverlag, 2004, pp. 179-184.
11. Paetz, J., Schneider, G. Virtual screening using local neuro-fuzzy rules. Proc. of the 13th
IEEE Int. Conf. on Fuzzy Systems, Budapest, Hungary, 2004, pp. 861-865.

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12.

13.

14.

15.

16.

17.

18.

19.

20.

21.

22.

23.

24.

25.

26.

27.

Schneider, G. (2003) Complexity challenges research in molecular informatics. In:
Molecular Informatics: Confronting Complexity (C. Kettner, M. Hicks; Eds). Logos Verlag,
Berlin, 2003, pp. 209-212.
Lavé, T., Luttringer, O., Zuegge, J., Schneider, G., Coassolo, P., Theil, F. P. Predictionof human pharmacokinetics based on in vitro and in vivo preclinical data. Ernst Schering
Res. Found. Workshop 37, 2001, pp. 81‐104.
Eglen, R., Schneider, G., Böhm, H. J. High‐ throughput screening: A virtual reality? In:
Virtual Screening for Bioactive Molecules (H. J. Böhm, G. Schneider; eds) Wiley‐VCH,
Weinheim, 2000, pp. 1‐14.
Schneider, G. Evolutionary search for bioactive molecules in virtual fitness landscapes.
In: Virtual Screening for Bioactive Molecules (H. J. Böhm, G. Schneider; eds) Wiley‐
VCH, Weinheim, 2000, pp. 161‐186.
Eglen, R., Schneider, G., Böhm, H. J. High‐ throughput screening: A virtual reality? In:
Virtual Screening for Bioactive Molecules (H. J. Böhm, G. Schneider; eds) Wiley‐VCH,
Weinheim, 2000, pp. 1‐14.
Wrede, P., Schneider, G. Generation of biased peptide libraries based on evolutionary
constraints. In: From Symbiosis to Eukaryotism - Endocytobiology VII (E. Wagner, J.
Normann, H. Greppin, J.H.P. Hackstein, R.G. Herrmann, K.V. Kowallik, H.E.A. Schenk,
J. Seckbach; eds), Geneva University Press, Geneva, 1999, pp. 579‐587.
Schneider, G., Broger, C. Visualization of protein sequence space by self‐organizing
neural networks ‐ Classification of protein targeting signals. In: From Symbiosis to
Eukaryotism - Endocytobiology VII (E. Wagner, J. Normann, H. Greppin, J.H.P.
Hackstein, R.G. Herrmann, K.V. Kowallik, H.E.A. Schenk, J. Seckbach; eds), Geneva
University Press, Geneva, 1999, pp. 589‐602.
Schneider, G., Schuchhardt, J., Malik, A., Glienke, J., Jagla, B., Behrens, D., Müller, S.,
Müller, G., Wrede, P. Analysis of mitochondrial and chloroplast targeting signals by
neural network systems. In: Eukaryotism and Symbiosis (H.E.A. Schenk, R. Herrmann,
K. W. Jeon, N. E. Müller, W. Schwemmler; eds), Springer‐Verlag, Berlin, Heidelberg,
1997, pp. 214‐229.
Schneider, G., Schneider, P., Wrede, P. Forward and inverted protein folding by
empirical property profiles and evolutionary algorithms. Software Development in
Chemistry 11 (G. Fels, V. Schubert; eds), GDCh, Frankfurt, 1997.
Malik, A., Schuchhardt, J., Schneider, G., Wrede, P. DNA‐sequence analysis byPerceptrons: Identification of splice‐ sites in human DNA. In: Software Development in
Chemistry 10 (J. Gasteiger; ed.), GDCh, Frankfurt, 1996, pp. 217‐236.
Müller, S., Schneider, G., Herbold, C., Schuchhardt, J., Müller, G., Wrede, P. ProFI: A
tool for amino acid sequence analysis by artificial neural networks. In: Software
Development in Chemistry 10 (J. Gasteiger; ed.), GDCh, Frankfurt, 1996, pp. 265‐ 270.
Schneider, G., Schuchhardt, J., Wrede, P. Classification of dipeptides by artificial neuralnetworks with different activation functions. In: Software Development in Chemistry 9 (R.
Moll; ed.), GDCh, Frankfurt, 1995, pp. 49‐64.
Schuchhardt, J., Schneider, G., Reichelt J., Schomburg, D., Wrede, P. Classification of
local structural motifs of proteins by Kohonen‐networks. In: Bioinformatics: From Nucleic
Acids and Proteins to Cell Metabolism (D. Schomburg, U. Lessel; eds), VCH, Weinheim,
1995, pp. 85‐92.
Schneider, G., Wrede, P. The rational design of peptides by artificial neural networks
and simulated molecular evolution. In: Software‐Development in Chemistry 8 (C.
Jochum; ed.), GDCh, Frankfurt, 1994, pp. 265‐280.
Schneider, G., Lohmann, R., Wrede, P. The rational design of amino acid sequences.
In: Concepts in Protein Engineering and Design (P. Wrede, G. Schneider; eds), Walter‐de‐Gruyter, Berlin, 1994, pp. 281‐317.
Schneider, G., Wrede, P. Analyse von Aminosäuresequenzen mit künstlichen
neuronalen Filtern. In: Software-Entwicklung in der Chemie 7 (D. Ziessow; ed.),Springer‐Verlag, Berlin, 1993, pp. 45‐51.
10Gisbert Schneider • Publications
28.

29.

30.

Schneider, G., Wrede, P. Zielgerichtete Synthese von Aminosäuresequenzen mit
künstlichen neuronalen Netzen. In: Grundlagen und Anwendungen der Künstlichen
Intelligenz (O. Herzog, T. Christaller, D. Schütt; eds), Springer‐Verlag, Berlin, 1993, pp.
326‐338.
Wrede, P., Schneider, G. Ein alternativer Protein‐ Design Zyklus. In: SoftwareEntwicklung in der Chemie 7 (D. Ziessow; ed.), Springer‐Verlag, Berlin, 1993, pp. 169‐
173.
Wrede, P., Schneider, G., Schwemmler, W. Protein targeting as an important process incell evolution. In: Endocytobiology V (S. Sato, M. Ishida, H. Ishikwa; eds), University
Press, Tübingen, 1993, pp. 567‐574.

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