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Journal of Cheminformatics, Volume 4 - Supplement
Volume 4, Number S-1, May 2012
- Frank Oellien, Uli Fechner, Thomas Engel
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GCC2011 - 25 years of computational chemistry meetings. 1
- Martin Brehm, Barbara Kirchner:
TRAVIS - a free analyzer and visualizer for Monte Carlo and molecular dynamics trajectories. 1 - Thorsten Meinl:
What's new in KNIME? 2 - Martin Pippel, Michael Scharfe, René Meier, Wolfgang Sippl:
ParaDockS - an open source framework for molecular docking. 3 - Michael Banck:
Packaging free software chemistry programs in Debian GNU/Linux: past, present and future. 4 - Johann Gasteiger:
25 years of CIC - achievements and future goals. 1 - Oliver Kohlbacher:
CADDSuite - a workflow-enabled suite of open-source tools for drug discovery. 2 - Anne Mai Wassermann, Jürgen Bajorath:
A computational method to facilitate structure-activity relationship transfer. 3 - Matthias Hilbig, Matthias Rarey:
Aligning chemical structure diagrams with local search. 4 - Colin R. Groom:
Chemoinformatics in drug development. 5 - Richard Marchese Robinson, Robert C. Glen, John B. O. Mitchell:
Winnow based identification of potent hERG inhibitors in silico: comparative assessment on different datasets. 6 - Jörg Degen, Mark Rogers-Evans, Daniel Stoffler:
Putting the available chemical space to the fingertips of our scientists. 7 - Johannes Schwöbel, Bruno Bienfait, Johann Gasteiger, Thomas Kleinöder, Jörg Marusczyk, Oliver Sacher, Christof H. Schwab, Aleksey Tarkhov, Lothar Terfloth, Mark T. D. Cronin:
Quantifying intrinsic chemical reactivity of molecular structural features for protein binding and reactive toxicity, using the MOSES chemoinformatics system. 8 - Jochen Heil, Roland Frach, Stefan M. Kast:
Non-continuum solvation using the EC-RISM method applied to predict tautomer ratios, pKa and enantiomeric excess of alkylation reactions. 9 - Christopher Reynolds
Integrating logic-based machine learning and virtual screening to discover new drugs. 10 - Daniel Moser, Joanna Wisniewska, Steffen Hahn, Estel la Buscató, Franca-Maria Klingler, Janosch Achenbach, Bettina Hofmann, Dieter Steinhilber, Ewgenij Proschak:
Design of dual ligands using excessive pharmacophore query alignment. 11 - Volker Hähnke
Text-based similarity searching for hit- and lead-candidate identification. 12 - Eva Rauls:
Understanding nanostructure formation from first principles. 13 - Andreas Klamt:
Solvent-screening and co-crystal screening for drug development with COSMO-RS. 14 - Bernd Doser, Marcus A. Neumann:
Assessment of a variety of dispersion-corrected density functional theory calculations used in molecular crystal structure prediction. 15 - Colin R. Batchelor
Semantics vs. statistics in chemical markup. 16 - Valentina Eigner-Pitto, Josef Eiblmaier, Hans Kraut, Larisa Isenko, Heinz Saller, Peter Loew:
ChemProspector and generic structures: advanced mining and searching of chemical content. 17 - John M. Barnard, Geoffrey M. Downs:
Recent and current developments in handling Markush structures from chemical patents. 18 - Herbert Köppen:
Computational chemistry in pharmaceutical research - where do we stand after 25 years? 19 - Li-hsing Wang, Andreas Evers, Peter Monecke, Thorsten Naumann:
Ligand based lead generation - considering chemical accessibility in rescaffolding approaches via BROOD. 20 - Oliver Koch:
Blocking protein-protein interactions: the identification of repetitive turn structures as basis for inhibitor building blocks. 21 - Xavier Barril:
Improvements in docking scoring functions: the physics-based perspective. 22 - Woldeamanuel A. Birru, Dallas B. Warren, Christopher J. H. Porter, Colin W. Pouton, David K. Chalmers:
Molecular modeling of lipid drug formulations. 23 - Peter-Paul Heym, Wolfgang Brandt, Ludger A. Wessjohann
Virtual screening for plant PARP inhibitors - what can be learned from human PARP inhibitors? 24
- Jan Alán, Petr Kulhánek, Jaroslav Koca:
Virtual screening and in silico design of novel inhibitors of bacterial lectins. 1 - Adrià Cereto-Massagué, Santiago Garcia-Vallvé, Gerard Pujadas:
DecoyFinder, a tool for finding decoy molecules. 2 - Artem Cherkasov:
Targeting protein-protein interactions using methods of cheminformatics. 3 - Dilyana Dimova, Jürgen Bajorath:
Design of multi-target activity landscapes that capture hierarchical activity cliff distributions. 4 - Lian Duan, Janna Hastings, Paula de Matos, Marcus Ennis, Christoph Steinbeck:
Structured chemical class definitions and automated matching for chemical ontology evolution. 5 - Roland Frach, Jochen Heil, Stefan M. Kast:
Structure and thermodynamics of nonaqueous solvation by integral equation theory. 6 - Simone Fulle, M. Stuart Armstrong, Paul W. Finn, Garrett M. Morris:
Assessment of a probabilistic framework for combining structure- and ligand-based virtual screening. 7 - Sascha K. Goll, Daniel Himmel, Ivo Leito, Ingo Krossing
Applying the unified pH scale: absolute acidities in the gas phase and anchor points for eleven representative liquid media. 8 - Verena Gossen, Gerhard Raabe, Markus Albrecht:
Mechanistic DFT studies - helicate-type complexes with different alcylic spacers. 9 - Christoph Grebner, Johannes Becker, Daniel Weber, Bernd Engels:
Tabu search based global optimization algorithms for problems in computational chemistry. 10 - Robert Günther, Peter Brust:
Synergistic approach of structure-based and ligand-based drug design for the development of selective cannabinod receptor ligands. 11 - Kathrin Heikamp, Anne Mai Wassermann, Jürgen Bajorath:
Potency-directed similarity searching using support vector machines. 12 - Stephen R. Heller:
Status of the InChI algorithm and InChI trust. 13 - Angela M. Henzler, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey:
A flexible-hydrogen interaction model for protein-ligand docking. 14 - Wolf-Dietrich Ihlenfeldt:
Revisiting the dataflow principle for chemical information processing. 15 - Petr Kacer, Jirí Václavík, Jan Prech, Marek Kuzma:
Asymmetric transfer hydrogenation of imines and ketones using chiral Ru(II)Cl(η6-p-cymene)[(S, S)-N-TsDPEN] catalyst: a computational study. 16 - Robert Kiss, Mark Sandor, Ferenc Szalai:
http://Mcule.com: a public web service for drug discovery. 17 - Andreas Klamt, Karin Wichmann, Michael Thormann:
COSMOsim3D for drug-similarity, alignment, and molecular field analysis. 18 - Alexander Klenner, Sandra Bergmann, Marc Zimmermann
Large scale chemical patent mining with UIMA and UNICORE. 19 - Florian Koelling, Knut Baumann:
CavKAHYBRID - between hard spheres and Gaussians. 20 - Georg Birkenheuer, Dirk Blunk
MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment. 21 - Alexander Kos:
From eScience to iScience "I want Answers not Links" - new ways to search the Internet. 22 - Patrick Markt, Gerhard Dürnberger, Jacques Colinge, Stefan Kubicek:
CLOUD - CeMM library of unique drugs. 23 - José L. Medina-Franco, Austin B. Yongye, Jaime Pérez-Villanueva, Richard A. Houghten, Karina Martínez-Mayorga:
Activity-difference maps and consensus similarity measure characterize structure-activity relationships. 24 - Jakyung Yoo, José L. Medina-Franco:
Computer-guided discovery of epigenetics drugs: molecular modeling and identification of inhibitors of DNMT1. 25 - Fabian López-Vallejo, Jacob Waddell, Austin B. Yongye, Richard A. Houghten, José L. Medina-Franco:
A large scale classification of molecular fingerprints for the chemical space representation and SAR analysis. 26 - Richard Moha, Verena Gossen:
Computer-aided studies of molecular structure-comparison of measured and computed ECD spectra. 27 - Britta Nisius, Sha Fan, Holger Gohlke:
Novel binding pocket descriptors based on DrugScore potential fields encoded by 3D Zernike descriptors. 28 - Dmitry I. Osolodkin, Liubov I. Kozlovskaya, Galina G. Karganova, Evgenia V. Dueva, Vladimir A. Palyulin, Nikolai S. Zefirov, Vladimir M. Pentkovski:
Computational studies of flaviviruses: approaching to novel fusion inhibitors. 29 - Ashish Pandey, Satyaprakash Tripathi, C. Gopi Mohan:
Identification of hot-spot regions of N-type Ca2+ channel receptor by homology modeling and molecular dynamics study, for structure-based blocker design. 30 - Lisa Peltason, Daniel Stoffler:
SAR Analyzer: a tool for interactive SAR data visualization and navigation. 31 - Florian D. Roessler, Oliver Korb, Andreas Bender, Werner Maentele, Peter J. Bond
Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment. 32 - Matthias Rupp, Alexandre Tkatchenko, Klaus-Robert Müller
Modeling of molecular atomization energies using machine learning. 33 - Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex:
The assessment of computationally derived protein ensembles in protein-ligand docking. 34 - Michael Scharfe, Martin Pippel, Wolfgang Sippl:
Development of target-biased scoring functions for protein-ligand docking. 35 - Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey:
Systematic search for pairwise dependencies of torsion angles. 36 - Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca:
QSPR designer - employ your own descriptors in the automated QSAR modeling process. 37 - Kai Stueckenschneider, Achim Zielesny, Gerhard Schembecker:
Adsorption of amino acids on MFI-type zeolite: DFT calculations and experimental results. 38 - Tim ten Brink, Ionut Onila, Adam Mazur, Oliver Korb, Heiko M. Möller, Christian Griesinger, Teresa Carlomagno, Thomas E. Exner:
Guiding protein-ligand docking with different experimental NMR-data. 39 - Jonathan D. Tyzack, Hamse Y. Mussa, Robert C. Glen:
Probabilistic classifier: generated using randomised sub-sampling of the feature space. 40 - Susann Vorberg, Ina Koch, Christian Buning:
Sodium dependent glucose transporter (SGLT) 1 / 2 - elucidating inhibitor SAR and selectivity using homology modelling and 3D QSAR studies. 41 - Kanin Wichapong, Wolfgang Sippl:
Postprocessing of molecular docking poses using binding free energy calculations. 42 - Jörg-Hubertus Wilhelm:
MyChemise: a 2D drawing software that uses morphing for visualisation purposes. 43 - Sabrina Wollenhaupt, Knut Baumann:
INSARA: a new method for the analysis and visualization of Structure-Activity-Relationships. 44 - Baljinder K. Grewal, Masilamani Elizabeth Sobhia:
In silico identification of novel PKC βII inhibitors: ligand and receptor based pharmacophore modeling, virtual screening, and molecular dynamics study. 45 - Uzma Mahmood, Zaheer-ul-Haq:
Docking based 3D-QSAR studies applied at the BRAF inhibitors to understand the binding mechanism. 46 - Petra O. Nnamani
Preliminary characterization of N-trimethylchitosan as a nanocarrier for malarie vaccine. 47 - Sangeetha Subramaniam, Monica Mehrotra, Dinesh Gupta:
Development of target focused library against drug target of P. falciparum using SVM and Molecular docking. 48 - Sebastian Rubert, Christian Gamroth, André J. Heissmann, Gunther Lukat, Ralf Rotzoll, Alexander Schäfer, Jens Krüger, Björn Sommer:
The GMX-Plugin for the CELLmicrocosmos MembraneEditor. 49 - Jan Kuras, Bailey Fallon
Open access: changing the way chemistry is published. 50 - Christian Tyrchan, Sorel Muresan
How often do follow-on activities occur - trends seen in a patent database for GPCRs. 51 - Stefan Kuhn, Nils E. Schlörer
From chemical shift data through prediction to assignment and NMR LIMS - multiple functionalities of nmrshiftdb2. 52 - Marta Pinto, Gerhard F. Ecker:
A computational model for predicting the transport of compounds by ABCC2. 53 - Barbara Zdrazil, Andreas Jurik, Regina Reicherstorfer, Thomas Stockner, Harald H. Sitte, Gerhard F. Ecker:
Insights into binding events of GABA- and Tiagabine- analogues in the Gamma-Aminobutyric Acid Transporter 1 by means of Molecular Modelling. 54 - Robert Körner, Iurii Sushko, Sergii Novotarskyi, Igor V. Tetko:
In silico pKa prediction. 55 - Waldemar Hujo, Stefan Grimme:
Performance of dispersion-corrected density functional theory for thermochemistry and non-covalent interactions. 56 - Janosch Achenbach, Franca-Maria Klingler, Steffen Hahn, Svenja Steinbrink, Mirjam Schroeder, Frank Loehr, Volker Dötsch, Dieter Steinhilber, Ewgenij Proschak:
Fragment-based identification of multi-target ligands by self-organizing map alignment. 57 - Manuela S. Murgueitio, Sandra Santos-Sierra, Gerhard Wolber:
Discovery of novel TLR modulators by Molecular Modeling and Virtual Screening. 58 - David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. 59 - Deepti Jaiswal Kundu, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca:
Searching for tunnels of proteins - comparison of approaches and available software tools. 60 - Stanislav Geidl, Roman Beránek, Radka Svobodová Vareková, Tomás Bouchal, Miroslav Brumovský, Michal Kudera, Ondrej Skrehota, Jaroslav Koca:
How the methodology of 3D structure preparation influences the quality of QSPR models? 61 - Ahmed Abdelaziz, Iurii Sushko, Wolfram Teetz, Robert Körner, Sergii Novotarskyi, Igor V. Tetko
QSAR modeling for In vitro assays: linking ToxCast™ database to the integrated modeling framework "OCHEM". 62
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