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Journal 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
Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma. 3 - Janna Hastings
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
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
Improved chemical text mining of patents using infinite dictionaries, translation and automatic spelling correction. 16 - Jens Krüger
Molecular simulation grid. 17 - Gerhard Klebe:
On the validity of popular assumptions in computational drug design. 18 - Violeta I. Pérez-Nueno, Vishwesh Venkatraman
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
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
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
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
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
QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. 16 - Vladimir A. Palyulin, Dmitry I. Osolodkin
Virtual screening workflow for glycogen synthase kinase 3β inhibitors: convergence of ligand-based and structure-based approaches. 17 - Johannes Schwöbel, Judith C. Madden
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
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. 20 - Paul Czodrowski
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
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
Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections. 27 - Sonja Herres-Pawlis
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
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
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
Brute-force pharmacophore assessment and scoring with Open3DQSAR. 39 - Stefan Mordalski
Homology modelling of metabotropic glutamate receptor 2. 40 - Rafal Kurczab
Evaluation of different machine learning methods for ligand-based virtual screening. 41 - Tomasz Kosciólek, Stefan Mordalski
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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