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Journal of Cheminformatics, Volume 6 - Supplement
Volume 6, Number S-1, March 2014
- Uli Fechner:
9th German Conference on Chemoinformatics. 1 - Alex Clark:
Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices. 1 - Thomas E. Exner, Andrea Frank, Heiko M. Möller, Martin Dracínský:
Can quantum-chemical NMR chemical shifts be used as criterion for force-field development. 2 - Karen T. Schomburg, Matthias Rarey
:
Facing the challenges of computational target prediction. 3 - Peter Ertl
Visualization of chemical space for medicinal chemists. 4 - Noel M. O'Boyle, Roger A. Sayle
What compound should I make next? Using Matched Molecular Series for prospective medicinal chemistry. 5 - Christian Kramer, Klaus R. Liedl
Limits to molecular matched-pair analysis: the experimental uncertainty case. 6 - Sebastian Stüker:
An automatic system for the simultaneous translation of lectures. 7 - Klaus R. Liedl
Entropy in specificity and thermodynamics of binding. 8 - Robert Günther
Development of cannabinoid receptor (CB 2 R) ligands for application in PET studies - where to attach the radiolabel? 9 - Ahmed M. El Kerdawy
Quantum-mechanics-based molecular interaction fields for 3D-QSAR. 10 - Gisbert Schneider:
Go with the flow and accessorize your drugs. 11 - Andreas Spitzmüller
Identification of host interactions for phenotypic antimalarial hits. 12 - Thorsten Meinl, Bernd Wiswedel, Michael R. Berthold:
Looking over the rim: algorithms for cheminformatics from computer scientists. 13 - Anne Mai Wassermann:
Structure-activity relationship analysis on the basis of matched molecular pairs. 14 - Christin Rakers
Combining pharmacophore- and MD-based modelling for phase II metabolism prediction. 15 - Fredrick Robin Devadoss, Victor Paul Raj:
Analysis and visual summarization of molecular dynamics simulation. 16 - Markus O. Zimmermann, Andreas Lange, Frank M. Boeckler
Validated scoring of halogen bonding in molecular design. 17 - Sabrina Wollenhaupt, Knut Baumann:
inSARa: intuitive single-target (large-scale) SAR interpretation and multi-target cross-reactivity analysis. 18 - Tim Clark:
Simulating "soft" electronics. 19 - Walter Langel
New insights on the interface between metal oxide and biosystem. 20 - Jacco Van de Streek:
Computational pharmaceutical materials science. 21 - Jérémie Mortier
Balancing selectivity vs stability using molecular dynamics and umbrella sampling. 22 - Gunther Lukat, Björn Sommer, Jens Krüger:
Membrane simulation analysis using Voronoi tessellation. 23 - Frank M. Boeckler
Use of DEKOIS 2.0 to gain insights for virtual screening. 24 - Ewgenij Proschak:
In silico polypharmacology: retrospective recognition vs. rational design. 25 - Tina Ritschel, Tom J. J. Schirris
KRIPO - a structure-based pharmacophores approach explains polypharmacological effects. 26 - Bekhelifa Leila, Zizi Zahia, Hallouch Mustapha, BenAhmed Abdellatif:
Determination of selected cetyltrimethylammonium halide parameters by molecular modeling. Study of their adsorption on montmorillonite. 1 - Lydia Rhyman, Ponnadurai Ramasami, Luis R. Domingo:
Theoretical studies on cycloaddition reactions. 2 - Jürgen Vogt, Evgeny Popov, Rainer Rudert, Natalja Vogt:
MOGADOC: a database with 3D-structures. 3 - Stephen R. Heller:
InChI - the worldwide chemical structure standard. 4 - Antonio de la Vega de León, Jürgen Bajorath:
Compound optimization through data set-dependent chemical transformations. 5 - Daniel Cappel, Vassilios Myrianthopoulos, Emmanuel Mikros, Woody Sherman:
Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases. 6 - Nikolay T. Kochev, Ivan Bangov, Emil Petrov, Marina Moskovkina, Borislav Stoyanov:
Charge-related topological index - various chemoinformatics applications. 7 - Paolo Tosco, Nikolaus Stiefl, Gregory A. Landrum:
The integration of Open3DTOOLS into the RDKit and KNIME. 8 - Andreas Truszkowski, Annamaria Fiethen, Hubert Kuhn, Thomas Wiebringhaus, Achim Zielesny, Matthias Epple:
Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants. 9 - Patrick McCabe, Oliver Korb, Jason C. Cole, Robin Taylor:
Kernel density estimation of CSD distributions - an application to knowledge based molecular optimisation. 10 - Sergey B. Sosnin, Vladimir A. Palyulin, Nikolai S. Zefirov:
A new software for fragment-based QSAR and its applications. 11 - Jirí Barilla, M. Lokajícek, H. Pisaková, Pavel Simr:
Simulation of the influence of oxygen on the chemical stage of radiobiological mechanism using Petri nets. 12 - Norbert Furtmann
Evaluation of molecular model-based discovery of ecto-5'-nucleotidase inhibitors on the basis of X-ray structures. 13 - Denis Fourches
Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software. 14 - Yen S. Low, Alexander Sedykh, Denis Fourches
Chemistry-wide association studies (CWAS) to determine joint toxicity effects of co-occurring chemical features. 15 - Andreas Lange
Scaffold dependencies for halogen bonding: quantum mechanical investigation of nitrogen-bearing heterocycles. 16 - Christian Herhaus:
Introducing fuzziness into maximum common substructures for meaningful cluster characterisation. 17 - Tim ten Brink, Clementine Aguirre, Isabelle Krimm:
Fragment docking supported by NMR shift perturbations. 18 - Tamer M. Ibrahim, Matthias R. Bauer
Probing the impact of protein and ligand preparation procedures on chemotype enrichment in structure-based virtual screening using DEKOIS 2.0 benchmark sets. 19 - Christoph Müller, Isabella Feierberg, Ola Engkvist
HTS explorer. 20 - Marius Nache, Rico Scheier, Heiner Schmidt, Bernd Hitzmann:
Meat quality prediction using Raman spectroscopy and chemometrics. 21 - Jakub Gunera, Peter Kolb:
Exploring and cataloguing the substrate space of prenyltransferases: automatic generation of SMARTS. 22 - Nitin Chitranshi, Pushpendra K. Tripathi, Prahlad K. Seth:
Interaction studies of Alzheimer's Cathepsin B protein with inhibitors in presence and absence of water. 23 - Bernd Rupp
DACS: from compound collections to rationally designed HTS library. 24 - Florent Chevillard, Peter Kolb:
De novo design of selective compounds: a fragment-based pipeline applied to the β2 adrenergic receptor. 25 - Tetyana Beltramo, Susanne Theuerl, Michael Klocke, Bernd Hitzmann:
Estimation of the biogas production rate, a chemometrical approach. 26 - Christoph Müller, Daniel L. Ormsby, Isabella Feierberg, Ola Engkvist
Hit series selection in noisy HTS data: clustering techniques, statistical tests and data visualisations. 27 - Kiran K. Telukunta, Xavier Lucas, Kersten Döring, Björn A. Grüning
Dynamic information system for small molecules. 28 - Péter Englert, Péter Kovács:
Making the most of approximate maximum common substructure search. 29 - Juan Carlos Mobarec
Computational modeling, docking and molecular dynamics of the transcriptional activator ComA bound to a newly-identified functional DNA binding site. 30 - Denis Schmidt, Peter Kolb:
Large-scale docking approaches to the kinome. 31 - Salwa M. Soliman, Gerhard Wolber:
Using structure- and Ligand-based pharmacophores as filters to discriminate Human Aryl Sulfotransferase 1A1 (SUL1A1) binders into substrates and inhibitors. 32 - Karsten Klein, Oliver Koch, Nils M. Kriege
Scaffold hunter: visual analysis of biological activity data. 33 - Wolf-Dietrich Ihlenfeldt:
Ushering the Cactvs Toolkit into the Python Age (without breaking the legacy). 34 - Mazen Ahmad, Olga V. Kalinina, Thomas Lengauer:
Entropy gain due to water release upon ligand binding. 35 - Eva Vennmann, Nadine Schneider, Gudrun Lange, Matthias Rarey
Elucidating protein-protein interactions using the HYDE scoring function. 36 - Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang:
Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach. 37 - Marwah Al Laila
Accelerating turbo similarity searching in chemoinformatics on multicore and GPU platforms. 38 - Petr Kacer, Sot Petr, Jan Pechacek, Jakub Januscak, Marek Kuzma:
Computational evaluation of the η6-arene during the ATH of imines on Noyori's RuII catalyst. 39 - Marcel Bermudez
Dualsteric modulators of the M2 muscarinic acetylcholine receptor. 40 - Deepti Jaiswal Kundu
Consistency of sugar structures and their annotation in the PDB. 41 - Doreen Mollenhauer, Nicola Gaston:
Towards understanding the chemical environment effect on gold-containing clusters. 42 - Jean-François Truchon, Kristina Grabowski, Barbara Sander, Alain Ajamian:
Exploiting solvent effects in drug design and optimization. 43 - Peter Schmidtke, Vincent Le Guilloux:
Fuzzy context specific matched molecular pairs. 44 - Timo Krotzky, Gerhard Klebe:
A new method for rapid comparison of protein binding pockets by capturing spatial distributions. 45 - 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. 46 - Daniel Reker, Tiago Rodrigues
Target prediction by cascaded self-organizing maps for ligand de-orphaning and side-effect investigation. 47 - Jens Kunze, Nickolay Todoroff, Tiago Rodrigues
Targeting flexibility: a structure-based computational study revealing allosteric HIV-1 protease inhibitors. 48 - Michael Reutlinger, Tiago Rodrigues
Go with the flow: de-orphaning focused combinatorial libraries. 49 - Jamil Al-Asri, Gerhard Wolber:
Discovery of novel α-amylase inhibitors using structure-based drug design. 50 - Xavier Lucas, Björn A. Grüning, Stefan Günther:
ChemicalToolBoX and its application on the study of the drug like and purchasable space. 51 - Katrin Stierand, Tim Harder, Lothar Wissler, Christian Lemmen, Matthias Rarey
Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web. 52 - Heike Thomas, Matthias Hennemann, Stefan Güssregen, Timothy Clark:
Parameterization to NDDO-based polarizable force field. 53 - Paul Labute, Markus Kossner, Alain Ajamian, Martin Santavy, Anna Lin:
Pharmacophore annotation using extended Hückel theory. 54 - Alexander Steudle, Rocco Varela, Ajay N. Jain:
Surflex-QMOD: physically meaningful QSAR. 55 - Anselm H. C. Horn, Danyil Huraskin, Heinrich Sticht:
Is there a sodium effect in fibrillar amyloid-β oligomers? 56 - José Batista, Paul C. D. Hawkins, Robert Tolbert, Matthew T. Geballe:
SiteHopper - a unique tool for binding site comparison. 57 - Hafida Chemouri, Sidi Mekelleche:
Theoretical illustration of the effect of 1-ethyl-pyridinium trifluoroacetate ionic liquid in the enhancement of the Diels-Alder reaction of isoprene with acrylic acid. 58 - Gunther Stahl, Paul C. D. Hawkins, Mark McGann, Matthew T. Geballe, Gregory L. Warren:
The application of statistical methods to cognate docking: A path forward? 59 - Tomás Bouchal, Radka Svobodová Vareková, Tomás Racek, Crina-Maria Ionescu, Stanislav Geidl, Ales Krenek, Jaroslav Koca:
Empirical charges for chemoinformatics applications. 60 - Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca:
QM quality atomic charges for proteins. 61 - Laura J. Kingsley
IterTunnel; a method for predicting and evaluating ligand EgressTunnels in proteins with buried active sites. 62
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