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ORCIDJournal of Cheminformatics, Volume 5 - Supplement
Volume 5, Number S-1, March 2013
- Uli Fechner:
8th German Conference on Chemoinformatics. 1
- Thorsten Meinl, Gregory A. Landrum:
Get your chemistry right with KNIME. 1 - Rebecca C. Wade:
Targeting protein dynamics in drug design. 1 - Felix Rausch, Wolfgang Brandt, Martin Schicht, Lars Bräuer, Friedrich Paulsen:
Protein modeling and molecular dynamic studies of two new surfactant proteins. 2 - Lars Packschies, Georg Birkenheuer, Dirk Blunk
, Sebastian Breuers, André Brinkmann, Ines dos Santos Vieira, Gregor Fels, Sandra Gesing, Richard Grunzke, Sonja Herres-Pawlis, Oliver Kohlbacher, Jens Krüger, Martin Kruse, Ulrich Lang, Ralph Müller-Pfefferkorn, Patrick Schäfer, Tobias Schlemmer, Thomas Steinke, Klaus-Dieter Warzecha, Andreas Zink:
The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment. 3 - Gregory A. Landrum:
Reproducibility in cheminformatics and computational chemistry research: certainly we can do better than this. 4 - Martin Vogt, Jürgen Bajorath:
Statistical modeling of value distributions of similarity coefficients in virtual screening and its application to predicting fingerprint search performance. 5 - Andrew Dalke, Janna Hastings:
FMCS: a novel algorithm for the multiple MCS problem. 6 - Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex:
How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening. 7 - Matthias Rarey, Adrian Kolodzik, Sascha Urbaczek:
Let's talk about rings. 8 - Richard Sherhod, Valerie J. Gillet, Thierry Hanser, Philip N. Judson, Jonathan D. Vessey:
Toxicological knowledge discovery by mining emerging patterns from toxicity data. 9 - Lucio Ciacchi:
Computational prediction of heterogeneous interface properties at the atomic level. 10 - Kai Stueckenschneider, Juliane Merz, Victor Milman, Gerhard Schembecker:
Theoretical and experimental study of the pH-dependent interaction of amino acids and MFI-type zeolite. 11 - Johannes Kirchmair, Andrew Howlett, Julio E. Peironcely, Daniel S. Murrell, Mark J. Williamson, Samuel E. Adams, Thomas Hankemeier, Leo van Buren, Guus Duchateau, Werner Klaffke, Robert C. Glen:
Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules. 12 - Paolo Tosco, Andreas Klamt:
3D-QSAR reloaded: Open3DALIGN meets COSMOsar3D. 13 - Andreas H. Göller:
Dataset overlap density analysis. 14 - Roger A. Sayle, José Batista, J. Andrew Grant:
Efficient maximum common subgraph (MCS) searching of large chemical databases. 15 - Guenter Grethe, Jonathan M. Goodman, Chad H. G. Allen:
International chemical identifier for chemical reactions. 16 - Klaus-Jürgen Schleifer:
Challenges in agrochemicals design. 17 - Charlotta Schärfe, Joachim Taeger, Peggy Reuter, Nina M. Fischer, Jens Krüger, Bernd Wissinger, Oliver Kohlbacher:
Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels. 18 - Martin Mosisch, Jan Simons, Lutz Hilterhaus, Andrew E. Torda:
Modifications to glucose-6-phosphate dehydrogenase for industrial applications: predictions and tests. 19
- Bahareh Honarparvar, Hendrik G. Kruger, Mahmoud E. S. Soliman, Glenn E. M. Maguire, Thavendran Govender:
Molecular modelling studies of synthesized pentacyclo-undecane peptides as potential HIV-1 wild type C-SA protease inhibitors. 1 - Dhiraj Sinha, Morteza Khabiri, David Reha, Rüdiger Ettrich:
In silico characterization of the motor subunit of the e.coli. restriction-modification system EcoR1241. 2 - Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey:
TorsionAnalyzer: exploring conformational space. 3 - Andreas Truszkowski, Annamaria Fiethen, Hubert Kuhn, Achim Zielesny, Matthias Epple:
Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD). 4 - Alexander Kos:
Automatic docking of a small number of ligands into a large number of binding sites. 5 - Florian Koelling:
PREDator - a new structure-based approach for cross-reactivity predictions. 6 - Peter Schmidtke, Ciantar Marine, Isabelle Theret, Pierre Ducrot:
Towards a complete structure of the hERG channel. 7 - Krzysztof Rataj, Jagna Witek, Stefan Mordalski, Tomasz Kosciólek, Andrzej J. Bojarski:
The importance of template choice in homology modeling. A 5-HT6R case study. 8 - Anna Kahler, Anselm H. C. Horn, Heinrich Sticht:
Stability of single and double layer fibrillar amyloid-β oligomers. 9 - Eileen Socher, Anselm H. C. Horn, Heinrich Sticht:
Is the novel amyloid-β tetramer fold a stable conformation? 10 - Michael Scharfe, Martin Pippel, Wolfgang Sippl:
ParaDockS - an open-source framework for molecular docking: implementation of target-class-specific scoring methods. 11 - Jakub Stepán, Petr Kulhánek, Milan Lenco, Zora Strelcová, Ales Krenek, Jaroslav Koca:
Nemesis - a molecular modeling package. 12 - Carina Jehn, Frank Schmidt-Döhl:
Simulation of transport processes and chemical reactions in building materials. 13 - Lennart Heinzerling, Matthias Rarey:
Force-field-based minimizations of protein-ligand complexes in the blink of an eye. 14 - Sonia Liggi, Alexios Koutsoukas, Yasaman Motamedi, Robert C. Glen, Andreas Bender:
Annotating targets with pathways: extending approaches to mode of action analysis. 15 - Stephen Maginn, Andrew Henry, Paul Labute, Johannes Maier, Nels Thorsteinson:
Efficient mining of protein kinase structural data. 16 - Sabrina Wollenhaupt, Knut Baumann:
Combination of fingerprints and MCS-based (inSARa) networks for Structure-Activity-Relationship analysis. 17 - Rucha K. Chiddarwar, Andreas Bender, Sebastian Rohrer:
In silico target prediction: identification of on- and off-targets for crop protection agents. 18 - Wolf-Dietrich Ihlenfeldt:
A next-generation chemistry database cartridge. 19 - Wolf-Dietrich Ihlenfeldt:
Taking the PubChem web sketcher to the next level. 20 - Benjamin Merget, David Zilian, Tobias Müller, Christoph A. Sotriffer:
MycPermCheck: the Mycobacterium tuberculosis permeability prediction tool for small molecules. 21 - Bastikar Virupaksha, Gupte Alpana, Khadke Prashant, Uday Deshpande, Alessandro Desideri:
Analysis of naphthoquinone derivatives as topoisomerase I inhibitors using fragment based QSAR. 22 - Sergii Novotarskyi, Iurii Sushko, Robert Körner, Igor V. Tetko:
Chemogenomic approach to increase accuracy of QSAR modeling of inhibition activity against five major P450 isoforms. 23 - Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A. Patel, Andreas Bender:
Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization. 24 - Sabina Smusz, Rafal Kurczab, Andrzej J. Bojarski:
The influence of hashed fingerprints density on the machine learning methods performance. 25 - Alexios Koutsoukas, Rubben Torella, George Drakakis, Andreas Bender, Robert C. Glen:
Relating GPCRs pharmacological space based on ligands chemical similarities. 26 - David Zilian, Christoph A. Sotriffer:
Combining SFCscore with Random Forests leads to improved affinity prediction for protein-ligand complexes. 27 - Jagna Witek, Krzysztof Rataj, Stefan Mordalski, Sabina Smusz, Tomasz Kosciólek, Andrzej J. Bojarski:
Application of Structural Interaction Fingerpints (SIFts) into post-docking analysis - insight into activity and selectivity. 28 - Timo Krotzky, Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier:
Extended graph-based models for enhanced similarity retrieval in Cavbase. 29 - Rafal Kurczab, Sabina Smusz, Andrzej J. Bojarski:
The influence of training actives/inactives ratio on machine learning performance. 30 - Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Andreas Bender, Adrián Velázquez-Campoy:
Experimental validation of in silico target predictions on synergistic protein targets. 31 - Barbara Zdrazil, Andreas Jurik, Harald H. Sitte, Gerhard F. Ecker:
Pairwise structural comparison of tiagabine analogs gives new insights into their protein binding modes. 32 - Désirée Baumann, Knut Baumann:
Reliable estimation of externally validated prediction errors for QSAR models. 33 - Georgios Drakakis, Alexios Koutsoukas, Suzanne Clare Brewerton, David A. Evans, Andreas Bender:
Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model. 34 - Susanne Eyrisch, Tobias Girschick, Günter Ross, Cédric Kalinski, Vladimir Khazak, Lutz Weber:
PriaXplore® - a novel technology platform for the identification of small molecule modulators of protein-protein interactions. 35 - Andrew Dalke:
The FPS fingerprint format and chemfp toolkit. 36 - Stephen R. Heller:
InChI - the worldwide chemical structure standard. 37 - Volker Hähnke, Evan Bolton, Stephen H. Bryant:
PubChem: atom environments for molecule standardization. 38 - Sebastian Radestock:
Optimising chemical information workflows: integrating Reaxys - use cases and applications. 39 - Robert Günther, Winnie Deuther-Conrad, Rares Moldovan, Steffen Fischer, Peter Brust:
A 3D-QSAR model for cannabinoid receptor (CB2) ligands derived from aligned pharmacophors. 40 - Luca Carlino, Martin Schmitt, Manfred Jung, Wolfgang Sippl:
Ligand-based and structure-based design of novel histone demethylase inhibitors. 41 - A. Tsoumanis, Georgia Melagraki, Antreas Afantitis:
Enalos KNIME nodes: exploring environmental durability, ageing resistance and corrosion inhibition. 42 - Janna Hastings, Pablo Conesa, Adriano Dekker, Marcus Ennis, Kenneth Haug, Kalai Vanii Jayaseelan, Namrata Kale, Tejasvi Mahendraker, Pablo A. Moreno, Venkatesh Muthukrishnan, Gareth I. Owen, Reza M. Salek, Steve Turner, Christoph Steinbeck:
Expanding natural product chemistry resources at the EBI. 43 - Fazlin Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Andreas Bender:
Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines. 44 - Oliver Koch:
More than a rigid framework: molecular design using secondary structure element information. 45 - V. Arulmozhi, Reghunadhan Rajesh:
Predicting the protein localization sites using artificial neural networks. 46 - V. Arulmozhi, Reghunadhan Rajesh:
Neural network based classification of acute toxicity of phthalate esters to fathead minnow. 47 - Stephen Maginn, Paul Labute, Alain Ajamian, Christopher I. Williams:
Rationalisation and visualisation of non-bonded interactions. 48 - Alexander Kos, Hans-Jürgen Himmler:
Finding unusual peptides on the internet using plain three letter sequence codes. 49 - Faisal Saeed, Naomie Salim, Ammar Abdo, Hamza Hentabli:
Using graph-based consensus clustering for combining K-means clustering of heterogeneous chemical structures. 50 - Ahmed Abdelaziz, Alexander Safanyaev, Vladimir A. Palyulin, Igor V. Tetko:
Building QSAR for HTS in vitro assays - a study for the prediction of Aryl hydrocarbon receptor activators. 51 - Petr Kacer, Jan Svoboda, Tereza Louzilova, Kamila Syslova, Marek Kuzma:
Pt(II) and Pt(IV) complexes with large hydrophobic ligands: a study of new potential cytostatics. 52 - Philipp Thiel, Lisa Peltason, Christian Ottmann, Oliver Kohlbacher:
Deterministic clustering of the available chemical space. 53
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