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ORCIDJournal of Cheminformatics, Volume 3 - Supplement
Volume 3, Number S-1, April 2011
- Frank Oellien, Uli Fechner, Thomas Engel
:
German Conference on Chemoinformatics 2010 - organizers' notes. 1
- Colleen Fitzpatrick:
Hand in the snow. 1 - Wolfgang Guba, Daniel Stoffler:
Cross-project HTS-datamining. 2 - Gregory A. Landrum, Richard A. Lewis, Andrew Palmer, Nikolaus Stiefl, Anna Vulpetti:
Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma. 3 - Janna Hastings, Nico Adams, Marcus Ennis, Duncan Hull, Christoph Steinbeck:
Chemical ontologies: what are they, what are they for and what are the challenges. 4 - Andrew R. Leach:
Cheminformatics and computational chemistry in lead optimisation. 5 - Christoph Steinbeck, Stefan Kuhn, Kalai Vanii Jayaseelan, Pablo A. Moreno:
Computational metabolomics - a field at the boundaries of cheminformatics and bioinformatics. 6 - Szabolcs Csepregi, Nóra Máté, Róbert Wágner, Tamás Csizmazia, Szilárd Dóránt, Erika Bíró, Tim Dudgeon, Ali Baharev, Ferenc Csizmadia:
Representation of Markush structures: from molecules toward patents. 7 - Matthias Rupp:
Graph kernels for chemoinformatics - a critical discussion. 8 - Daniel J. Warner, Stephen A. St-Gallay, Edward J. Griffen:
WizePairZ: a novel algorithm to identify, encode, and exploit matched molecular pairs with unspecified cores in medicinal chemistry. 9 - K. Friedemann Schmidt, Andreas Evers, Alexander Amberg, Gerhard Hessler, Catherine Robles, Karl-Heinz Baringhaus:
Phototoxicity - from molecular descriptors to classification models. 10 - Simone Fulle, Holger Gohlke:
Constraint counting on RNA and ribosomal structures: linking flexibility and function. 11 - Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey:
Chemical pattern visualization in 2D - the SMARTSviewer. 12 - Johannes G. E. M. Fraaije, Rubèn Serral Gracià:
Composite multiscale chemical informatics for formulations: challenges and solutions. 13 - Noel M. O'Boyle, Casey M. Campbell, Geoffrey R. Hutchison:
De novo design of molecular wires with optimal properties for solar energy conversion. 14 - Jürgen Gmehling:
Thermodynamic models and factual data banks - ideal tools for the development of chemical processes. 15 - Roger A. Sayle, Plamen Petrov, Jon Winter, Sorel Muresan:
Improved chemical text mining of patents using infinite dictionaries, translation and automatic spelling correction. 16 - Jens Krüger, Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Gregor Fels, Sandra Gesing, Richard Grunzke, Oliver Kohlbacher, Nico Kruber, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Sonja Herres-Pawlis, Patrick Schäfer, Hans-Günther Schmalz, Thomas Steinke, Klaus-Dieter Warzecha, Martin Wewior:
Molecular simulation grid. 17 - Gerhard Klebe:
On the validity of popular assumptions in computational drug design. 18 - Violeta I. Pérez-Nueno, Vishwesh Venkatraman, Lazaros Mavridis, David W. Ritchie:
Predicting drug polypharmacology using a novel surface property similarity-based approach. 19 - Kathryn Loving, Noeris K. Salam, Daniel Cappel, Woody Sherman:
Generation of structure-based pharmacophores using energetic analysis - application on fragment docking. 20 - Holger Gohlke, Alexander Metz, Christopher Pfleger, Dennis M. Krüger, Sina Kazemi:
Towards targeting protein-protein interfaces with small molecules. 21 - Hannes G. Wallnoefer, Torsten Lingott, José Gutiérrez, Irmgard Merfort, Klaus R. Liedl:
Backbone flexibility controls the activity and specificity of a protein-protein interface - specificity in snake venom metalloproteases (SVMPs). 22 - Oliver Koch, Daniel Cappel, Monika Nocker, Timo Jäger, Leopold Flohé, Christoph A. Sotriffer, Paul M. Selzer:
Virtual screening using structure-based consensus pharmacophore models and ensemble docking based on MD-generated conformations. 23 - Welchy Cavalcanti, Michael Hoffmann, Marc Amkreutz, Peter Schiffels:
Computational nanotechnology for functional coatings. 24
- Jianxin Duan, G. Madhavi Sastry, Steven L. Dixon, Jeffrey F. Lowrie, Woody Sherman:
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. 1 - Simone Lorenzi, Andrea Beccari, D. Carettoni, M. Rubino, Vanessa Nardese:
Discovering HDAC class II selective inhibitors by multidisciplinary approach. 2 - Boris Karulin, Mikhail Kozhevnikov:
Ketcher: web-based chemical structure editor. 3 - Dmitry Pavlov, Mikhail Rybalkin, Boris Karulin, Mikhail Kozhevnikov, Alexey Savelyev, A. Churinov:
Indigo: universal cheminformatics API. 4 - Andreas Truszkowski, Stefan Neumann, Achim Zielesny, Egon L. Willighagen, Christoph Steinbeck:
CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution. 5 - Brad Sherborne:
Free-Wilson in the 21st Century - evolution of a versatile toolkit for SAR analysis. 6 - Gert Thijs, Wilfried Langenaeker, Hans De Winter:
Application of spectrophores™ to map vendor chemical space using self-organising maps. 7 - Alexander Klenner, Michael Reutlinger, Gisbert Schneider:
Visualization and virtual screening in molecular property spaces. 8 - David W. Miller, Robert Fraczkiewicz, Walter S. Woltosz:
Novel ADMET design tool for chemists. 9 - Janosch Achenbach, Ewgenij Proschak:
Rational, computer-aided design of multi-target ligands. 10 - Hans-Christian Ehrlich, Matthias Rarey:
Searching substructures in fragment spaces. 11 - Andrew Dalke:
chemfp - fast and portable fingerprint formats and tools. 12 - Stefan Bietz, Sascha Urbaczek, Matthias Rarey:
Hydrogen placement in protein-ligand complexes under consideration of tautomerism. 13 - Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Ines dos Santos Vieira, Gregor Fels, Sandra Gesing, Richard Grunzke, Sonja Herres-Pawlis, Oliver Kohlbacher, Nico Kruber, Jens Krüger, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Patrick Schäfer, Hans-Günther Schmalz, Thomas Steinke, Klaus-Dieter Warzecha, Martin Wewior:
MoSGrid - a molecular simulation grid as a new tool in computational chemistry, biology and material science. 14 - Marcel Schumann, Marc Röttig, Nina M. Fischer, Oliver Kohlbacher:
A framework and workflow system for virtual screening and molecular docking. 15 - Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jaroslav Koca:
QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. 16 - Vladimir A. Palyulin, Dmitry I. Osolodkin, Nikolai S. Zefirov:
Virtual screening workflow for glycogen synthase kinase 3β inhibitors: convergence of ligand-based and structure-based approaches. 17 - Johannes Schwöbel, Judith C. Madden, Mark T. D. Cronin:
Application of a chemical reactivity database to predict toxicity for reactive mechanisms. 18 - Pablo A. Moreno, Kalai Vanii Jayaseelan, Christoph Steinbeck:
Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues. 19 - Iurii Sushko, Anil Kumar Pandey, Sergii Novotarskyi, Robert Körner, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko:
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. 20 - Paul Czodrowski, Chresten R. Søndergaard, Sebastian Dohm, Gerhard Klebe, Jens Erik Nielsen:
LigpKa - a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations. 21 - Ines dos Santos Vieira, Janna Börner, Ulrich Flörke, Sonja Herres-Pawlis:
Studies on the mechanism of the lactide polymerization with highly active zinc guanidine catalysts. 22 - Sascha K. Goll, Daniel Himmel, Ivo Leito, Ingo Krossing:
Quantum chemical calculations on a unified pH scale for all phases. 23 - Torsten Thalheim, Dominik Wondrousch, Stefanie Stöckl, Denis Mulliner, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
Diagnostic of tautomer behaviour on QSAR models and AM1 optimisation. 24 - Brigitta Elsässer, Gregor Fels:
Atomistic details of the phosphodiester cleavage of ribonuclease H. 25 - Fabian Bös, Ulrike Uhrig, Brian B. Masek, James R. Damewood:
Muse+TriposScore: a ligand-based de novo design approach. 26 - Alberto Del Rio, Arménio Jorge Moura Barbosa, Fabiana Caporuscio:
Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections. 27 - Sonja Herres-Pawlis, Roxana Haase, Olga Bienemann:
Dissecting the role of guanidine copper complexes in atom transfer radical polymerization by density functional theory. 28 - Nadine Schneider, Gudrun Lange, Robert Klein, Christian Lemmen, Matthias Rarey:
HYDEing the false positives - scoring for lead optimization. 29 - Adrián Kalászi, Gábor Imre, Miklós Vargyas:
Flexible alignment in 3D and its applications. 30 - Florian Koelling, Knut Baumann:
Cavka - a new automatic pharmacophore elucidation method in progress. 31 - Noel M. O'Boyle, Tim Vandermeersch, Geoffrey R. Hutchison:
Confab - generation of diverse low energy conformers. 32 - Srinivasaraghavan Kannan, Wolfgang Sippl, Martin Zacharias:
Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent. 33 - Jan Dreher, Knut Baumann:
Comparison of ATP binding sites using structure-based similarity methods and molecular interaction fields. 34 - Martin Pippel, René Meier, Wolfgang Sippl:
PARADOCKS - a framework for molecular docking. 35 - Dennis M. Krüger, José Ignacio Garzón, P. C. Montes, Holger Gohlke:
Predicting protein-protein interactions with DrugScorePPI: fully-flexible docking, scoring, and in silico alanine-scanning. 36 - Tina Ritschel, David J. Wood, Jacob de Vlieg, Markus Wagener:
Extraction of useful bioisostere replacments from the PDB. 37 - Michael Scharfe, Benjamin Maurer, Klaus Aktories, Manfred Jung, Wolfgang Sippl:
Docking and virtual screening of novel inhibitors for mono-ADP-ribosylating toxins. 38 - Paolo Tosco, Thomas Balle:
Brute-force pharmacophore assessment and scoring with Open3DQSAR. 39 - Stefan Mordalski, Tomasz Kosciólek, Aina Westrheim Ravna, Ingebrigt Sylte, Andrzej J. Bojarski:
Homology modelling of metabotropic glutamate receptor 2. 40 - Rafal Kurczab, Sabina Smusz, Andrzej J. Bojarski:
Evaluation of different machine learning methods for ligand-based virtual screening. 41 - Tomasz Kosciólek, Stefan Mordalski, Andrzej J. Bojarski:
Rapid binding site analysis by means of structural interaction fingerprint patterns - an implication to GPCR-targeted CADD. 42 - Björn Sommer, Tim Dingersen, Christian Gamroth, André J. Heissmann, Gunther Lukat, Ralf Rotzoll, Sebastian Rubert, Alexander Schäfer, Jens Krüger:
Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes. 43
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