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Predicting pK_a values from EEM atomic charges

The acid dissociation constant p K_ais a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p K_...

Authors: Radka Svobodová Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan and Jaroslav Koča

Citation: Journal of Cheminformatics 2013 5:18

Content type: Research article Published on: 10 April 2013
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The influence of the inactives subset generation on the performance of machine learning methods

A growing popularity of machine learning methods application in virtual screening, in both classification and regression tasks, can be observed in the past few years. However, their effectiveness is strongly d...

Authors: Sabina Smusz, Rafał Kurczab and Andrzej J Bojarski

Citation: Journal of Cheminformatics 2013 5:17

Content type: Research article Published on: 5 April 2013
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Pt(II) and Pt(IV) complexes with large hydrophobic ligands: a study of new potential cytostatics

Authors: Petr Kacer, Jan Svoboda, Tereza Louzilova, Kamila Syslova and Marek Kuzma

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P52

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Rationalisation and visualisation of non-bonded interactions

Authors: Stephen Maginn, Paul Labute, Alain Ajamian and Chris Williams

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P48

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Predicting the protein localization sites using artificial neural networks

Authors: V Arulmozhi and Rajesh Reghunadhan

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P46

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Enalos KNIME nodes: exploring environmental durability, ageing resistance and corrosion inhibition

Authors: A Tsoumanis, G Melagraki and A Afantitis

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P42

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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A 3D-QSAR model for cannabinoid receptor (CB2) ligands derived from aligned pharmacophors

Authors: Robert Günther, Winnie Deuther-Conrad, Rareś Moldovan, Steffen Fischer and Peter Brust

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P40

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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PubChem: atom environments for molecule standardization

Authors: Volker Hähnke, Evan E Bolton and Stephen H Bryant

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P38

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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The FPS fingerprint format and chemfp toolkit

Authors: Andrew Dalke

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P36

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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PriaXplore^® - a novel technology platform for the identification of small molecule modulators of protein-protein interactions

Authors: Susanne Eyrisch, Tobias Girschick, Günter Ross, Cédric Kalinski, Vladimir Khazak and Lutz Weber

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P35

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model

Authors: Georgios Drakakis, Alexios Koutsoukas, Suzanne Clare Brewerton, David DE Evans and Andreas Bender

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P34

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Reliable estimation of externally validated prediction errors for QSAR models

Authors: Désirée Baumann and Knut Baumann

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P33

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Pairwise structural comparison of tiagabine analogs gives new insights into their protein binding modes

Authors: Barbara Zdrazil, Andreas Jurik, Harald H Sitte and Gerhard F Ecker

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P32

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Experimental validation of in silico target predictions on synergistic protein targets

Authors: Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Andreas Bender and Adrian Velazquez-Campoy

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P31

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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The influence of training actives/inactives ratio on machine learning performance

Authors: Rafał Kurczab, Sabina Smusz and Andrzej J Bojarski

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P30

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Extended graph-based models for enhanced similarity retrieval in Cavbase

Authors: Timo Krotzky, Thomas Fober, Marco Mernberger, Gerhard Klebe and Eyke Hüllermeier

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P29

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Application of Structural Interaction Fingerpints (SIFts) into post-docking analysis - insight into activity and selectivity

Authors: Jagna Witek, Krzysztof Rataj, Stefan Mordalski, Sabina Smusz, Tomasz Kosciolek and Andrzej J Bojarski

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P28

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Combining SFCscore with Random Forests leads to improved affinity prediction for protein-ligand complexes

Authors: D Zilian and CA Sotriffer

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P27

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Relating GPCRs pharmacological space based on ligands chemical similarities

Authors: Alexios Koutsoukas, Rubben Torella, George Drakakis, Andreas Bender and Robert C Glen

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P26

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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The influence of hashed fingerprints density on the machine learning methods performance

Authors: Sabina Smusz, Rafał Kurczab and Andrzej J Bojarski

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P25

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Chemogenomic approach to increase accuracy of QSAR modeling of inhibition activity against five major P450 isoforms

Authors: Sergii Novotarskyi, Iurii Sushko, Robert Koerner and Igor V Tetko

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P23

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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MycPermCheck: the Mycobacterium tuberculosispermeability prediction tool for small molecules

Authors: Benjamin Merget, David Zilian, Tobias Müller and Christoph A Sotriffer

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P21

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Modifications to glucose-6-phosphate dehydrogenase for industrial applications: predictions and tests

Authors: Martin Mosisch, Jan Simons, Lutz Hilterhaus and Andrew Torda

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O19

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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A next-generation chemistry database cartridge

Authors: Wolf D Ihlenfeldt

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P19

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels

Authors: Charlotta PI Schärfe, Joachim Taeger, Peggy Reuter, Nina M Fischer, Jens Krüger, Bernd Wissinger and Oliver Kohlbacher

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O18

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Challenges in agrochemicals design

Authors: KJ Schleifer

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O17

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Combination of fingerprints and MCS-based (inSARa) networks for Structure-Activity-Relationship analysis

Authors: Sabrina Wollenhaupt and Knut Baumann

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P17

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Efficient maximum common subgraph (MCS) searching of large chemical databases

Authors: Roger A Sayle, Jose Batista and J Andrew Grant

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O15

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Annotating targets with pathways: extending approaches to mode of action analysis

Authors: Sonia Liggi, Alexios Koutsoukas, Yasaman Kalantar Motamedi, Robert C Glen and Andreas Bender

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P15

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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3D-QSAR reloaded: Open3DALIGN meets COSMOsar3D

Authors: Paolo Tosco and Andreas Klamt

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O13

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Simulation of transport processes and chemical reactions in building materials

Authors: Carina Jehn and Frank Schmidt-Döhl

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P13

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Theoretical and experimental study of the pH-dependent interaction of amino acids and MFI-type zeolite

Authors: Kai Stueckenschneider, Juliane Merz, Victor Milman and Gerhard Schembecker

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O11

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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ParaDockS - an open-source framework for molecular docking: implementation of target-class-specific scoring methods

Authors: Michael Scharfe, Martin Pippel and Wolfgang Sippl

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P11

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Toxicological knowledge discovery by mining emerging patterns from toxicity data

Authors: Richard Sherhod, Valerie J Gillet, Thierry Hanser, Philip N Judson and Jonathan D Vessey

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O9

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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The importance of template choice in homology modeling. A 5-HT₆R case study

Authors: Krzysztof Rataj, Jagna Witek, Stefan Mordalski, Tomasz Kościółek and Andrzej J Bojarski

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P8

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Let's talk about rings

Authors: Matthias Rarey, Adrian Kolodzik and Sascha Urbaczek

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O8

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening

Authors: Barbara Sander, Oliver Korb, Jason Cole and Jonathan W Essex

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O7

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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PREDator - a new structure-based approach for cross-reactivity predictions

Authors: Florian Koelling

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P6

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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FMCS: a novel algorithm for the multiple MCS problem

Authors: Andrew Dalke and Janna Hastings

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O6

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Statistical modeling of value distributions of similarity coefficients in virtual screening and its application to predicting fingerprint search performance

Authors: Martin Vogt and Jürgen Bajorath

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O5

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD)

Authors: Andreas Truszkowski, Annamaria Fiethen, Hubert Kuhn, Achim Zielesny and Matthias Epple

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P4

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Reproducibility in cheminformatics and computational chemistry research: certainly we can do better than this

Authors: Gregory A Landrum

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O4

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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TorsionAnalyzer: exploring conformational space

Authors: Christin Schärfer, Tanja Schulz-Gasch and Matthias Rarey

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P3

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment

Authors: 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…

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O3

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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In silico characterization of the motor subunit of the e.coli. restriction-modification system EcoR1241

Authors: Dhiraj Sinha, Morteza Khabiri, David Reha and Rudiger Ettrich

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P2

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Protein modeling and molecular dynamic studies of two new surfactant proteins

Authors: Felix Rausch, Wolfgang Brandt, Martin Schicht, Lars Bräuer and Friedrich Paulsen

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O2

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Molecular modelling studies of synthesized pentacyclo-undecane peptides as potential HIV-1 wild type C-SA protease inhibitors

Authors: Bahareh Honarparvar, Hendrik G Kruger, Mahmoud ES Soliman, Glenn EM Maguire and Thavendran Govender

Citation: Journal of Cheminformatics 2013 5(Suppl 1):P1

Content type: Poster presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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8th German Conference on Chemoinformatics

Authors: Uli Fechner

Citation: Journal of Cheminformatics 2013 5(Suppl 1):A1

Content type: Introduction Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Targeting protein dynamics in drug design

Authors: Rebecca C Wade

Citation: Journal of Cheminformatics 2013 5(Suppl 1):O1

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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Get your chemistry right with KNIME

Authors: Thorsten Meinl and Gregory Landrum

Citation: Journal of Cheminformatics 2013 5(Suppl 1):F1

Content type: Oral presentation Published on: 22 March 2013

This article is part of a Supplement: Volume 5 Supplement 1
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