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Books and Theses
- 1994
[b1]Gisbert Schneider:
Protein-Design in machina: künstliche neuronale Netze und simulierte molekulare Evolution. Free University of Berlin, Germany, Shaker 1994, ISBN 978-3-86111-830-5
Journal Articles
- 2024
- [j65]Stephan Allenspach
, Jan A. Hiss, Gisbert Schneider:
Neural multi-task learning in drug design. Nat. Mac. Intell. 6(2): 124-137 (2024) - 2023
- [j64]Agnieszka Ilnicka, Gisbert Schneider:
Designing molecules with autoencoder networks. Nat. Comput. Sci. 3(11): 922-933 (2023) - 2022
- [j63]Michael Moret, Francesca Grisoni, Paul Katzberger, Gisbert Schneider:
Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models. J. Chem. Inf. Model. 62(5): 1199-1206 (2022) - 2021
- [j62]José Jiménez-Luna, Miha Skalic, Nils Weskamp, Gisbert Schneider:
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment. J. Chem. Inf. Model. 61(3): 1083-1094 (2021) - [j61]Roberto Fino, Dominik Lenhart, Vishal C. Kalel, Charlotte A. Softley, Valeria Napolitano, Ryan Byrne, Wolfgang Schliebs, Maciej Dawidowski, Ralf Erdmann, Michael Sattler, Gisbert Schneider, Oliver Plettenburg, Grzegorz M. Popowicz:
Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2, 3, 4, 5-Tetrahydrobenzo[F][1, 4]oxazepines as Potential New Trypanocidal Agents. J. Chem. Inf. Model. 61(10): 5256-5268 (2021) - [j60]Kenneth Atz, Francesca Grisoni, Gisbert Schneider:
Geometric deep learning on molecular representations. Nat. Mach. Intell. 3(12): 1023-1032 (2021) - 2020
- [j59]Francesca Grisoni, Michael Moret, Robin Lingwood, Gisbert Schneider:
Bidirectional Molecule Generation with Recurrent Neural Networks. J. Chem. Inf. Model. 60(3): 1175-1183 (2020) - [j58]Alexander S. Rich, Cynthia Rudin, David M. P. Jacoby, Robin Freeman, Oliver R. Wearn, Henry Shevlin, Kanta Dihal, Seán S. ÓhÉigeartaigh, James Butcher, Marco Lippi, Przemyslaw Palka, Paolo Torroni, Shannon Wongvibulsin, Edmon Begoli, Gisbert Schneider, Stephen Cave, Mona Sloane, Emanuel Moss, Iyad Rahwan, Ken Goldberg, David Howard, Luciano Floridi, Jack Stilgoe:
AI reflections in 2019. Nat. Mach. Intell. 2(1): 2-9 (2020) - [j57]Michael Moret, Lukas Friedrich, Francesca Grisoni, Daniel Merk, Gisbert Schneider:
Generative molecular design in low data regimes. Nat. Mach. Intell. 2(3): 171-180 (2020) - [j56]José Jiménez-Luna, Francesca Grisoni, Gisbert Schneider:
Drug discovery with explainable artificial intelligence. Nat. Mach. Intell. 2(10): 573-584 (2020) - 2019
- [j55]Christoph Alexander Bauer, Gisbert Schneider, Andreas H. Göller:
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies. J. Cheminformatics 11(1): 59:1-59:16 (2019) - [j54]Gisbert Schneider:
Mind and machine in drug design. Nat. Mach. Intell. 1(3): 128-130 (2019) - [j53]Alexander Button, Daniel Merk, Jan A. Hiss, Gisbert Schneider:
Automated de novo molecular design by hybrid machine intelligence and rule-driven chemical synthesis. Nat. Mach. Intell. 1(7): 307-315 (2019) - 2018
- [j52]Alex T. Müller, Jan A. Hiss, Gisbert Schneider:
Recurrent Neural Network Model for Constructive Peptide Design. J. Chem. Inf. Model. 58(2): 472-479 (2018) - 2017
- [j51]Alex T. Müller, Gisela Gabernet, Jan A. Hiss, Gisbert Schneider:
modlAMP: Python for antimicrobial peptides. Bioinform. 33(17): 2753-2755 (2017) - 2016
- [j50]Hans Peter Lüthi, Stefan N. Heinen, Gisbert Schneider, Andreas Glöss, Martin P. Brändle, Rollin A. King, Edward Pyzer-Knapp, Fahhad H. Alharbi, Sabre Kais:
The quantum chemical search for novel materials and the issue of data processing: The InfoMol project. J. Comput. Sci. 15: 65-73 (2016) - 2014
- [j49]Gisbert Schneider:
Go with the flow and accessorize your drugs. J. Cheminformatics 6(S-1): 11 (2014) - [j48]Anna Maria Perna, Thomas Schmidt, Tim Fugmann, Nicole Tegtmeyer, Steffen Backert, Silja Wessler, Gisbert Schneider:
Peptide lineup against Gram-negative bacterial infection - first-in-class peptide inhibitor of H. pylori HtrA. J. Cheminformatics 6(S-1): 46 (2014) - [j47]Daniel Reker, Tiago Rodrigues, Petra Schneider, Gisbert Schneider:
Target prediction by cascaded self-organizing maps for ligand de-orphaning and side-effect investigation. J. Cheminformatics 6(S-1): 47 (2014) - [j46]Jens Kunze, Nickolay Todoroff, Tiago Rodrigues, Petra Schneider, Gisbert Schneider:
Targeting flexibility: a structure-based computational study revealing allosteric HIV-1 protease inhibitors. J. Cheminformatics 6(S-1): 48 (2014) - [j45]Michael Reutlinger, Tiago Rodrigues, Petra Schneider, Gisbert Schneider:
Go with the flow: de-orphaning focused combinatorial libraries. J. Cheminformatics 6(S-1): 49 (2014) - [j44]Jens Kunze, Nickolay Todoroff, Petra Schneider, Tiago Rodrigues, Tim Geppert, Felix Reisen, Herman Schreuder, Joachim Saas, Gerhard Hessler, Karl-Heinz Baringhaus, Gisbert Schneider:
Targeting Dynamic Pockets of HIV-1 Protease by Structure-Based Computational Screening for Allosteric Inhibitors. J. Chem. Inf. Model. 54(3): 987-991 (2014) - [j43]Matthias Rupp, Matthias R. Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M. Boeckler, Gisbert Schneider:
Machine Learning Estimates of Natural Product Conformational Energies. PLoS Comput. Biol. 10(1) (2014) - 2013
- [j42]Christian P. Koch, Anna Maria Perna, Max Pillong, Nickolay K. Todoroff, Paul Wrede, Gerd Folkers, Jan A. Hiss, Gisbert Schneider:
Scrutinizing MHC-I Binding Peptides and Their Limits of Variation. PLoS Comput. Biol. 9(6) (2013) - 2012
- [j41]Gisbert Schneider:
Designing the molecular future. J. Comput. Aided Mol. Des. 26(1): 115-120 (2012) - [j40]Tim Geppert, Felix Reisen, Max Pillong, Volker Hähnke, Yusuf Tanrikulu, Christian P. Koch, Anna Maria Perna, Tatiana Batista Perez, Petra Schneider, Gisbert Schneider:
Virtual screening for compounds that mimic protein-protein interface epitopes. J. Comput. Chem. 33(5): 573-579 (2012) - [j39]Markus Hartenfeller, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber, Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, Steffen Renner:
Probing the Bioactivity-Relevant Chemical Space of Robust Reactions and Common Molecular Building Blocks. J. Chem. Inf. Model. 52(5): 1167-1178 (2012) - [j38]Markus Hartenfeller, Heiko Zettl, Miriam Walter, Matthias Rupp, Felix Reisen, Ewgenij Proschak, Sascha Weggen, Holger Stark, Gisbert Schneider:
DOGS: Reaction-Driven de novo Design of Bioactive Compounds. PLoS Comput. Biol. 8(2) (2012) - 2011
- [j37]Dragos Horvath, Christian J. Koch, Gisbert Schneider, Gilles Marcou, Alexandre Varnek:
Local neighborhood behavior in a combinatorial library context. J. Comput. Aided Mol. Des. 25(3): 237-252 (2011) - [j36]Volker Hähnke, Alexander Klenner, Friedrich Rippmann, Gisbert Schneider:
Pharmacophore alignment search tool: Influence of the third dimension on text-based similarity searching. J. Comput. Chem. 32(8): 1618-1634 (2011) - [j35]Volker Hähnke, Gisbert Schneider:
Pharmacophore alignment search tool: Influence of scoring systems on text-based similarity searching. J. Comput. Chem. 32(8): 1635-1647 (2011) - [j34]Alexander Klenner, Michael Reutlinger, Gisbert Schneider:
Visualization and virtual screening in molecular property spaces. J. Cheminformatics 3(S-1): 8 (2011) - [j33]Michael Bieler, Ralf Heilker, Herbert Köppen, Gisbert Schneider:
Assay Related Target Similarity (ARTS) - Chemogenomics Approach for Quantitative Comparison of Biological Targets. J. Chem. Inf. Model. 51(8): 1897-1905 (2011) - [j32]Markus Hartenfeller, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber, Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, Steffen Renner:
A Collection of Robust Organic Synthesis Reactions for In Silico Molecule Design. J. Chem. Inf. Model. 51(12): 3093-3098 (2011) - 2010
- [j31]Tim Geppert, Ewgenij Proschak, Gisbert Schneider:
Protein-protein docking by shape-complementarity and property matching. J. Comput. Chem. 31(9): 1919-1928 (2010) - [j30]Volker Hähnke, Matthias Rupp, Mireille Krier, Friedrich Rippmann, Gisbert Schneider:
Pharmacophore alignment search tool: Influence of canonical atom labeling on similarity searching. J. Comput. Chem. 31(15): 2810-2826 (2010) - [j29]Matthias Rupp, Timon Schroeter, Ramona Steri, Ewgenij Proschak, Katja Hansen, Heiko Zettl, Oliver Rau, Manfred Schubert-Zsilavecz, Klaus-Robert Müller, Gisbert Schneider:
Kernel learning for ligand-based virtual screening: discovery of a new PPARγ agonist. J. Cheminformatics 2(S-1): 27 (2010) - [j28]Sarah Keppner, Ewgenij Proschak, Gisbert Schneider, Birgit Spänkuch:
SBE13, a newly identified inhibitor of inactive polo-like kinase 1. J. Cheminformatics 2(S-1): 54 (2010) - 2009
- [j27]Jan A. Hiss, Gisbert Schneider:
Architecture, function and prediction of long signal peptides. Briefings Bioinform. 10(5): 569-578 (2009) - [j26]Bjoern A. Krueger, Tanja Weil, Gisbert Schneider:
Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists. J. Comput. Aided Mol. Des. 23(12): 869-881 (2009) - [j25]Volker Hähnke, Bettina Hofmann, Tomislav Grgat, Ewgenij Proschak, Dieter Steinhilber, Gisbert Schneider:
PhAST: Pharmacophore alignment search tool. J. Comput. Chem. 30(5): 761-771 (2009) - [j24]Matthias Rupp, Petra Schneider, Gisbert Schneider:
Distance phenomena in high-dimensional chemical descriptor spaces: Consequences for similarity-based approaches. J. Comput. Chem. 30(14): 2285-2296 (2009) - [j23]Felix Reisen, Gisbert Schneider, Ewgenij Proschak:
Reaction-MQL: Line Notation for Functional Transformation. J. Chem. Inf. Model. 49(1): 6-12 (2009) - 2008
- [j22]Andreas Schüller, Marcel Suhartono, Uli Fechner, Yusuf Tanrikulu, Sven Breitung, Ute Scheffer, Michael W. Göbel, Gisbert Schneider:
The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA. J. Comput. Aided Mol. Des. 22(2): 59-68 (2008) - [j21]Ewgenij Proschak, Matthias Rupp, Swetlana Derksen, Gisbert Schneider:
Shapelets: Possibilities and limitations of shape-based virtual screening. J. Comput. Chem. 29(1): 108-114 (2008) - [j20]Andreas Schüller, Gisbert Schneider:
Identification of Hits and Lead Structure Candidates with Limited Resources by Adaptive Optimization. J. Chem. Inf. Model. 48(7): 1473-1491 (2008) - 2007
- [j19]Ewgenij Proschak, Jörg K. Wegner, Andreas Schüller, Gisbert Schneider, Uli Fechner:
Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching. J. Chem. Inf. Model. 47(2): 295-301 (2007) - [j18]Uli Fechner, Gisbert Schneider:
Flux (2): Comparison of Molecular Mutation and Crossover Operators for Ligand-Based de Novo Design. J. Chem. Inf. Model. 47(2): 656-667 (2007) - [j17]Matthias Rupp, Ewgenij Proschak, Gisbert Schneider:
Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity. J. Chem. Inf. Model. 47(6): 2280-2286 (2007) - 2006
- [j16]Michael Meissner, Michael Schmuker, Gisbert Schneider:
Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training. BMC Bioinform. 7: 125 (2006) - [j15]Uli Fechner, Gisbert Schneider:
Flux (1): A Virtual Synthesis Scheme for Fragment-Based de Novo Design. J. Chem. Inf. Model. 46(2): 699-707 (2006) - [j14]Alexander Böcker, Gisbert Schneider, Andreas Teckentrup:
NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening. J. Chem. Inf. Model. 46(6): 2220-2229 (2006) - [j13]Steffen Renner, Christof H. Schwab, Johann Gasteiger, Gisbert Schneider:
Impact of Conformational Flexibility on Three-Dimensional Similarity Searching Using Correlation Vectors. J. Chem. Inf. Model. 46(6): 2324-2332 (2006) - 2005
- [j12]Jürgen Paetz, Gisbert Schneider:
A neuro-fuzzy approach to virtual screening in molecular bioinformatics. Fuzzy Sets Syst. 152(1): 67-82 (2005) - [j11]Alexander Böcker, Swetlana Derksen, Elena Schmidt, Andreas Teckentrup, Gisbert Schneider:
A Hierarchical Clustering Approach for Large Compound Libraries. J. Chem. Inf. Model. 45(4): 807-815 (2005) - 2004
- [j10]Evgeny Byvatov, Gisbert Schneider:
SVM-Based Feature Selection for Characterization of Focused Compound Collections. J. Chem. Inf. Model. 44(3): 993-999 (2004) - 2003
- [j9]Uli Fechner, Lutz Franke, Steffen Renner, Petra Schneider, Gisbert Schneider:
Comparison of correlation vector methods for ligand-based similarity searching. J. Comput. Aided Mol. Des. 17(10): 687-698 (2003) - [j8]Evgeny Byvatov, Uli Fechner, Jens Sadowski, Gisbert Schneider:
Comparison of Support Vector Machine and Artificial Neural Network Systems for Drug/Nondrug Classification. J. Chem. Inf. Comput. Sci. 43(6): 1882-1889 (2003) - 2000
- [j7]Gisbert Schneider, Man-Ling Lee, Martin Stahl, Petra Schneider:
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J. Comput. Aided Mol. Des. 14(5): 487-494 (2000) - [j6]Gisbert Schneider:
Neural networks are useful tools for drug design. Neural Networks 13(1): 15-16 (2000) - 1999
- [j5]Martin Stahl, Daniel Bur, Gisbert Schneider:
Mapping of proteinase active sites by projection of surface-derived correlation vectors. J. Comput. Chem. 20(3): 336-347 (1999) - 1996
- [j4]Gisbert Schneider, Johannes Schuchhardt, Paul Wrede:
Evolutionary optimization in multimodal search space. Biol. Cybern. 74(3): 203-207 (1996) - 1995
- [j3]Gisbert Schneider, Johannes Schuchhardt, Paul Wrede:
Development of simple fitness landscapes for peptides by artificial neural filter systems. Biol. Cybern. 73(3): 245-254 (1995) - 1994
- [j2]Gisbert Schneider, Tilman Todt, Paul Wrede:
De novo design of peptides and proteins: machine-generated sequences by the PROSA program. Comput. Appl. Biosci. 10(1): 75-77 (1994) - [j1]Gisbert Schneider, Johannes Schuchhardt, Paul Wrede:
Artificial neural networks and simulated molecular evolution are potential tools for sequence-oriented protein design. Comput. Appl. Biosci. 10(6): 635-645 (1994)
Conference and Workshop Papers
- 2004
- [c4]Jürgen Paetz, Gisbert Schneider:
Virtual screening using local neuro-fuzzy rules. FUZZ-IEEE 2004: 861-865 - 1997
- [c3]Johannes Schuchhardt, H. Rystedt, Gisbert Schneider, Uwe Hobohm, Paul Wrede:
Automatic classification of Loop-Structures in Proteins by an Unsupervised Neural Network. German Conference on Bioinformatics 1997: 183-184 - 1994
- [c2]Gisbert Schneider, Paul Wrede:
Optimizing Amino Acid Sequences by Simulated Molecular Evolution. Parcella 1994: 335-346 - 1993
- [c1]Gisbert Schneider, Paul Wrede:
Zielgerichtetes Design von Aminosäuresequenzen mit Künstlichen Neuronalen Netzen. KI 1993: 326-337
Informal and Other Publications
- 2022
- [i3]Clemens Isert, Kenneth Atz, Gisbert Schneider:
Structure-based drug design with geometric deep learning. CoRR abs/2210.11250 (2022) - 2021
- [i2]Kenneth Atz, Francesca Grisoni, Gisbert Schneider:
Geometric Deep Learning on Molecular Representations. CoRR abs/2107.12375 (2021) - 2020
- [i1]José Jiménez-Luna, Francesca Grisoni, Gisbert Schneider:
Drug discovery with explainable artificial intelligence. CoRR abs/2007.00523 (2020)
Coauthor Index
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