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Journal of Cheminformatics, Volume 2 - Supplement
Volume 2, Number S-1, May 2010
- Frank Oellien, Uli Fechner, Thomas Engel:
5th German Conference on Chemoinformatics: 23. CIC-Workshop. November 8-10, 2009, Goslar, Germany. 1
- Dmitry Pavlov, Mikhail Rybalkin, Boris Karulin:
Bingo from SciTouch LLC: chemistry cartridge for Oracle database. 1 - Mikhail Kozhevnikov, Boris Karulin:
Dingo: 2D molecule and reaction structural formula rendering library. 2 - Mark Rijnbeek:
OrChem. 3
- Günter von Kiedrowski:
Systems chemistry: from chemical self-replication to trisoligo-based nanoconstruction. 1 - Eberhard O. Voit:
The role of systems modeling in drug discovery and predictive health. 2 - Gerard J. P. van Westen
, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Molecular bioactivity extrapolation to novel targets by support vector machines. 3 - Joseph L. Durant, William Lingran Chen, Bradley D. Christie, David L. Grier, Burton A. Leland, James G. Nourse:
Representation and searching of biomolecules. 4 - Knut Baumann:
Cross-validation is dead. Long live cross-validation! Model validation based on resampling. 5 - Dragos Horvath, Gilles Marcou, Alexandre Varnek:
A unified approach to the applicability domain problem of QSAR models. 6 - Rob D. Brown, J. Dana Honeycutt, Sarah L. Aaron:
Quantifying model errors using similarity to training data. 7 - Torsten Thalheim, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
A Branch-and-Bound approach for tautomer enumeration. 8 - Carsten Detering, Holger Claussen, Marcus Gastreich
KnowledgeSpace - a publicly available virtual chemistry space. 9 - Gerhard Wolber, Thomas Seidel, Fabian Bendix:
3D pharmacophore alignments: does improved geometric accuracy affect virtual screening performance? 10 - Frank Tristram:
The protein flexibility in receptor-ligand docking simulations. 11 - José Batista:
Random molecular substructures as fragment-type descriptors. 12 - Thomas Kostka:
Making people's lives easier, better and more beautiful - and how computer-aided materials design may help. 13 - Carsten Wittekindt, Hubert Kuhn:
Biomaterialcoatings - a challenging task studied by the molecular fragment dynamics. 14 - Sonja Herres-Pawlis, Janna Börner, Ines dos Santos Vieira, Ulrich Flörke:
Mechanistic studies on the ring-opening polymerisation of D, L-lactide with zinc guanidine complexes. 15 - Antony J. Williams, Valery Tkachenko, Sergey Golotvin, Richard Kidd, Graham McCann:
ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry. 16 - Adel Golovin, Kim Henrick, Gerard J. Kleywegt:
Integration of chemical information with protein sequences and 3D structures. 17 - Oliver Koepler, Wolf-Tilo Balke, Benjamin Köhncke, Irina Sens, Sascha Tönnies:
Personalized information spaces: improved access to chemical digital libraries. 18 - Karl-Heinz Baringhaus, Gerhard Hessler, Thomas Klabunde:
Current aspects and future trends of computer-aided rescaffolding. 19 - Wolfgang Brandt, Julia Kufka, Diana Schulze, Eva Schulze, Felix Rausch, Ludger A. Wessjohann
The membrane bound aromatic p-hydroxybenzoic acid oligoprenyltransferase (UbiA) - how iterative improvements lead to a realistic structure that offers new insights into functional aspects of prenyl transferases and terpene synthases. 20 - Björn Sommer, Tim Dingersen, Sebastian E. Schneider, Sebastian Rubert, Christian Gamroth:
CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes. 21 - Christoph A. Sotriffer:
Approaching the limits: scoring functions for affinity prediction. 22 - Jens Krüger, Gregor Fels:
Ion permeation through neuronal nAChR ion channel. 23 - Markus Wagener, Sander B. Nabuurs, Jacob de Vlieg:
Fleksy: a flexible approach to induced fit docking. 24
- Alexander Kos
CWM global search - an internet search engine for the chemist. 1 - Stephen R. Heller, Alan McNaught:
The status of the InChI project and the InChI trust. 2 - Lian Duan:
jsMolEditor: an open source molecule editor for the next generation web. 3 - Bernd Wendt, Fabian Bös, Ulrike Uhrig:
Mining public-source databases for structure-activity relationships. 4 - Sergii Novotarskyi, Iurii Sushko, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Volodymyr V. Prokopenko, Igor V. Tetko
OCHEM - on-line CHEmical database & modeling environment. 5 - Paula de Matos, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Steve Turner, Christoph Steinbeck
ChEBI: a chemistry ontology and database. 6 - Christian Tyrchan, Sorel Muresan
Comparing manual and automated extraction of chemical entities from documents. 7 - Igor Grbavac, Oliver Koepler, S. Dohmeyer-Fischer, Gregor Fels, Irina Sens, Jan Brase:
Embedded infrastructure for primary data in chemistry. 8 - Stefanie Stöckl, Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
Prediction of the partition coefficient between air and body compartments from the chemical structure. 9 - Haiying Yu, Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
Modelling dissociation constants of organic acids by local molecular parameters. 10 - Andrea Volkamer, Thomas Grombacher, Matthias Rarey
Where are the boundaries? Automated pocket detection for druggability studies. 11 - Francisco Torrens, Gloria Castellano:
Protein negative/positively cooperative binding to zwitterionic/anionic vesicles. 12 - Mikhail Rudenko, Andreì L. Tchougréeff:
CARTESIUS: a group function based toolkit for hybrid molecular modelling. 13 - Hubert Kuhn, Stefan Neumann, Christoph Steinbeck, Carsten Wittekindt, Achim Zielesny:
Molecular fragments chemoinformatics. 14 - Catherine Michaux, Johan Wouters, Denis Jacquemin, Eric A. Perpète:
A theoretical investigation of microhydration of amino acids. 15 - Olaf van den Hoven, Gerard J. P. van Westen
Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models. 16 - Gerhard Hessler, Oliver Korb, Peter Monecke, Thomas Stützle, Thomas E. Exner:
pharmACOphore: multiple flexible ligand alignment based on ant colony optimization. 17 - Michael C. Hutter, Markus Krier:
Bioisosteric similarity of drugs in virtual screening. 18 - Tomas Öberg
Updating existing QSAR models: selection and weighting of new data. 19 - Dennis M. Krüger, Holger Gohlke:
DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR. 20 - Eugen Lounkine, Jürgen Bajorath:
Adaptation of formal concept analysis for the systematic exploration of structure-activity and structure-selectivity relationships. 21 - Mathias Wawer, Lisa Peltason, Jürgen Bajorath:
Systematic extraction of structure-activity relationship information from biological screening data. 22 - Horacio Emilio Pérez Sánchez, Bernhard Fischer, Daria B. Kokh, Holger Merlitz, Wolfgang Wenzel:
High throughput in-silico screening against flexible protein receptors. 23 - Oliver Koch, Timo Jäger, Leopold Flohé, Paul M. Selzer:
Virtual screening by high-throughput docking using hydrogen bonding constraints for targeting a protein-protein interface in M. tuberculosis. 24 - Oliver Korb, Simon Bowden, Tjelvar S. G. Olsson, David Frenkel, John W. Liebeschuetz, Jason C. Cole:
Ensemble docking revisited. 25 - Peter T. A. Galek, Frank H. Allen, László Fábián:
Picking out polymorphs: H-bond prediction and crystal structure stability. 26 - Matthias Rupp, Timon Schroeter, Ramona Steri, Ewgenij Proschak, Katja Hansen, Heiko Zettl, Oliver Rau, Manfred Schubert-Zsilavecz, Klaus-Robert Müller
Kernel learning for ligand-based virtual screening: discovery of a new PPARγ agonist. 27 - Mark Rijnbeek, Christoph Steinbeck:
OrChem: an open source chemistry search engine for Oracle. 28 - Ksenia Oguievetskaia, Laetitia Martin-Chanas, Artem Vorotyntsev, Olivia Doppelt-Azeroual, Xavier Brotel, Stewart A. Adcock, Alexandre G. de Brevern
Computational fragment-based drug design to explore the hydrophobic subpocket of the mitotic kinesin Eg5 allosteric binding site. 29 - Gilles Marcou, Nicolas Lachiche, L. Brillet, J.-M. Paris, Alexandre Varnek:
Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset. 30 - Fabian Bös, K. M. Smith, Q. Liu:
Multi-parameter scoring functions for ligand- and structure-based de novo design. 31 - Thomas Seidel, Gerhard Wolber:
Ligand-side tautomer enumeration and scoring for structure-based drug-design. 32 - Thorsten Meinl, Claude Ostermann, Olaf Nimz, Andrea Zaliani
Maximum-score diversity selection for early drug discovery. 33 - Stefan Kuhn, Christoph Steinbeck:
Progress on an open source computer-assisted structure elucidation suite (SENECA). 34 - Michael Hsing, Kendall G. Byler, Artem Cherkasov:
Prediction of highly-connected 'hub'-proteins in protein interaction networks using QSAR. 35 - Georg Hinselmann, Nikolas Fechner, Andreas Jahn, Andreas Zell:
Efficient extraction of canonical spatial relationships using a recursive enumeration of k-subsets. 36 - Cornelis Matijssen:
A comparative study of in silico prediction of pKa. 37 - Nikolas Fechner, Georg Hinselmann, Andreas Jahn, Andreas Zell:
Kernel-based estimation of the applicability domain of QSAR models. 38 - Julio E. Peironcely, Andreas Bender, Miguel Rojas-Chertó, Theo H. Reijmers, Leon Coulier, Thomas Hankemeier
Expanding and understanding metabolite space. 39 - Sergii Novotarskyi, Iurii Sushko, Robert Körner, Anil Kumar Pandey, Igor V. Tetko
Classification of CYP450 1A2 inhibitors using PubChem data. 40 - Iurii Sushko, Sergii Novotarskyi, Anil Kumar Pandey, Robert Körner, Igor V. Tetko
Applicability domain for classification problems. 41 - Andreas Jahn, Hannes Planatscher, Georg Hinselmann, Nikolas Fechner, Andreas Zell:
Automatic pharmacophore model generation using weighted substructure assignments. 42 - Tim ten Brink, Thomas E. Exner:
A combined combinatorial and pKa-based approach to ligand protonation states. 43 - Alexander Entzian, Horst Bögel, Mirko Buchholz
Semi-empirical derived descriptors for the modelling of properties of N-containing heterocycles. 44 - Veronica R. Khayrullina, Horst Bögel:
QSAR of anti-inflammatory drugs. 45 - Luca Pireddu
Fingerprint-based detection of acute aquatic toxicity. 46 - Axel J. Soto, Marc Strickert, Gustavo E. Vazquez
Adaptive matrix metrics for molecular descriptor assessment in QSPR classification. 47 - Eelke van der Horst, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich
Evolutionary design of selective adenosine receptor ligands. 48 - Vladimir A. Palyulin, Eugene V. Radchenko, Dmitry I. Osolodkin, Vladimir I. Chupakhin
Ionotropic GABA receptors: modelling and design of selective ligands. 49 - Katrin Stierand, Matthias Rarey
PoseView - molecular interaction patterns at a glance. 50 - Jeroen Kazius:
Get the best from substructure mining. 51 - Nina M. Fischer, Wolfgang M. Schneider, Oliver Kohlbacher:
Rescoring of docking poses using force field-based methods. 52 - Miguel Rojas-Chertó, Piotr T. Kasper, Julio E. Peironcely, Theo H. Reijmers, Rob J. Vreeken
The pipelined metabolite identification based on MS fragmentation. 53 - Sarah Keppner, Ewgenij Proschak, Gisbert Schneider, Birgit Spänkuch:
SBE13, a newly identified inhibitor of inactive polo-like kinase 1. 54
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