Volume 6; Issue 1 Suppleme

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Journal of Cheminformatics
Volume 6; Issue 1 Suppleme

Journal of Cheminformatics

Volume 6; Issue 1 Suppleme

1

9th German Conference on Chemoinformatics

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 382 KB

english, 2014

2

Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 64 KB

english, 2014

3

Quantum-mechanics-based molecular interaction fields for 3D-QSAR

ElKerdawy, Ahmed, Güssregen, Stefan, Matter, Hans, Hennemann, Matthias, Clark, Timothy

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 232 KB

english, 2014

4

Go with the flow and accessorize your drugs

Schneider, Gisbert

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

5

Identification of host interactions for phenotypic antimalarial hits

Spitzmüller, Andreas, Mestres, Jordi

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 75 KB

english, 2014

6

Looking over the rim: algorithms for cheminformatics from computer scientists

Meinl, Thorsten, Wiswedel, Bernd, Berthold, Michael R

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

7

Structure-activity relationship analysis on the basis of matched molecular pairs

Wassermann, Anne

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 71 KB

english, 2014

8

Combining pharmacophore- and MD-based modelling for phase II metabolism prediction

Rakers, Christin, Wolber, Gerhard

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

9

Analysis and visual summarization of molecular dynamics simulation

Devadoss, Fredrick, Paul Raj, Victor

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 78 KB

english, 2014

10

Validated scoring of halogen bonding in molecular design

Zimmermann, MO, Lange, A, Boeckler, FM

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 201 KB

english, 2014

11

inSARa: intuitive single-target (large-scale) SAR interpretation and multi-target cross-reactivity analysis

Wollenhaupt, Sabrina, Baumann, Knut

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

12

Simulating “soft” electronics

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

13

Can quantum-chemical NMR chemical shifts be used as criterion for force-field development

Exner, Thomas E, Frank, Andrea, Möller, Heiko M, Dračínský, Martin

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

14

New insights on the interface between metal oxide and biosystem

Langel, Walter, Köppen, Susan, Friedrichs, Wenke, Marx, Armin, Ohler, Bastian

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

15

Computational pharmaceutical materials science

van de Streek, Jacco

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

16

Balancing selectivity vs stability using molecular dynamics and umbrella sampling

Mortier, Jeremie, Nyakatura, Elisabeth K, Miettinen, Markus, Baldauf, Carsten, Wolber, Gerhard, Koksch, Beate

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 201 KB

english, 2014

17

Membrane simulation analysis using Voronoi tessellation

Lukat, Gunther, Sommer, Björn, Krüger, Jens

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 177 KB

english, 2014

18

Use of DEKOIS 2.0 to gain insights for virtual screening

Boeckler, Frank M, Bauer, Matthias R, Ibrahim, Tamer M, Vogel, Simon M

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

19

In silico polypharmacology: retrospective recognition vs. rational design

Proschak, Ewgenij

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

20

KRIPO – a structure-based pharmacophores approach explains polypharmacological effects

Tina Ritschel,Tom JJ Schirris,Frans GM Russel

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

21

Facing the challenges of computational target prediction

Schomburg, Karen T, Rarey, Matthias

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

22

Visualization of chemical space for medicinal chemists

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

23

What compound should I make next? Using Matched Molecular Series for prospective medicinal chemistry

O’Boyle, Noel M, Sayle, Roger, Boström, Jonas

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 103 KB

english, 2014

24

Limits to molecular matched-pair analysis: the experimental uncertainty case

Kramer, Christian, Liedl, Klaus

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 71 KB

english, 2014

25

An automatic system for the simultaneous translation of lectures

Stüker, Sebastian

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

26

Entropy in specificity and thermodynamics of binding

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 64 KB

english, 2014

27

Development of cannabinoid receptor (CB 2 R) ligands for application in PET studies - where to attach the radiolabel?

Günther, Robert, Moldovan, Rareş, Lueg, Corinna, Deuther-Conrad, Winnie, Wünsch, Bernhard, Brust, Peter

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 99 KB

english, 2014

28

Determination of selected cetyltrimethylammonium halide parameters by molecular modeling. Study of their adsorption on montmorillonite

Leila, Bekhelifa, Zahia, Zizi, Mustapha, Hallouch, Abdellatif, BenAhmed

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 66 KB

english, 2014

29

Kernel density estimation of CSD distributions - an application to knowledge based molecular optimisation

McCabe, Patrick, Korb, Oliver, Cole, Jason, Taylor, Robin

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

30

A new software for fragment-based QSAR and its applications

Sosnin, Sergey B, Palyulin, Vladimir A, Zefirov, Nikolay S

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

31

Simulation of the influence of oxygen on the chemical stage of radiobiological mechanism using Petri nets

Barilla, J, Lokajíček, M, Pisaková, H, Simr, P

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 66 KB

english, 2014

32

Evaluation of molecular model-based discovery of ecto-5’-nucleotidase inhibitors on the basis of X-ray structures

Furtmann, Norbert, Bajorath, Jürgen

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 75 KB

english, 2014

33

Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software

Fourches, Denis, Tropsha, Alexander

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 68 KB

english, 2014

34

Chemistry-wide association studies (CWAS) to determine joint toxicity effects of co-occurring chemical features

Low, Yen, Sedykh, Alexander, Fourches, Denis, Tropsha, Alexander

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

35

Scaffold dependencies for halogen bonding: quantum mechanical investigation of nitrogen-bearing heterocycles

Lange, A, Zimmermann, MO, Boeckler, MF

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 106 KB

english, 2014

36

Introducing fuzziness into maximum common substructures for meaningful cluster characterisation

Herhaus, Christian

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 71 KB

english, 2014

37

Fragment docking supported by NMR shift perturbations

Brink, Tim, Aguirre, Clementine, Krimm, Isabelle

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 75 KB

english, 2014

38

Probing the impact of protein and ligand preparation procedures on chemotype enrichment in structure-based virtual screening using DEKOIS 2.0 benchmark sets

Ibrahim, Tamer M, Bauer, Matthias R, Boeckler, Frank M

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 222 KB

english, 2014

39

Theoretical studies on cycloaddition reactions

Rhyman, Lydia, Ramasami, Ponnadurai, Domingo, Luis R

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

40

HTS explorer

Müller, Christoph, Feierberg, Isabella, Engkvist, Ola, Tyrchan, Christian

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 76 KB

english, 2014

41

Meat quality prediction using Raman spectroscopy and chemometrics

Nache, Marius, Scheier, Rico, Schmidt, Heiner, Hitzmann, Bernd

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

42

Exploring and cataloguing the substrate space of prenyltransferases: automatic generation of SMARTS

Gunera, Jakub, Kolb, Peter

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 491 KB

english, 2014

43

Interaction studies of Alzheimer's Cathepsin B protein with inhibitors in presence and absence of water

Chitranshi, Nitin, Tripathi, Pushpendra K, Seth, Prahlad K

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 280 KB

english, 2014

44

DACS: from compound collections to rationally designed HTS library

Rupp, Bernd, Al-Yamori, Raed, Pawletta, Martyna, Lisurek, Michael, Kühne, Ronald

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 68 KB

english, 2014

45

De novo design of selective compounds: a fragment-based pipeline applied to the β2 adrenergic receptor

Chevillard, Florent, Kolb, Peter

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

46

Estimation of the biogas production rate, a chemometrical approach

Beltramo, Tetyana, Theuerl, Susanne, Klocke, Michael, Hitzmann, Bernd

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

47

Hit series selection in noisy HTS data: clustering techniques, statistical tests and data visualisations

Müller, Christoph, Ormsby, Daniel, Feierberg, Isabella, Engkvist, Ola, Tyrchan, Christian, Hartshorn, Michael J

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 76 KB

english, 2014

48

Dynamic information system for small molecules

Telukunta, Kiran K, Lucas, Xavier, Döring, Kersten, Grüning, Björn A, Günther, Stefan

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

49

Making the most of approximate maximum common substructure search

Englert, Péter, Kovács, Péter

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 57 KB

english, 2014

50

MOGADOC: a database with 3D-structures

Vogt, Jürgen, Popov, Evgeny, Rudert, Rainer, Vogt, Natalja

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 140 KB

english, 2014

51

Computational modeling, docking and molecular dynamics of the transcriptional activator ComA bound to a newly-identified functional DNA binding site

Mobarec, Juan C, Wolf, Diana, Bischofs, Ilka B, Kolb, Peter

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 59 KB

english, 2014

52

Large-scale docking approaches to the kinome

Schmidt, Denis, Kolb, Peter

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

53

Using structure- and Ligand-based pharmacophores as filters to discriminate Human Aryl Sulfotransferase 1A1 (SUL1A1) binders into substrates and inhibitors

Soliman, Salwa M, Wolber, Gerhard

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

54

Scaffold hunter: visual analysis of biological activity data

Klein, Karsten, Koch, Oliver, Kriege, Nils, Mutzel, Petra, Schäfer, Till

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 262 KB

english, 2014

55

Ushering the Cactvs Toolkit into the Python Age (without breaking the legacy)

Ihlenfeldt, Wolf D

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

56

Entropy gain due to water release upon ligand binding

Ahmad, Mazen, Kalinina, Olga, Lengauer, Thomas

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

57

Elucidating protein-protein interactions using the HYDE scoring function

Vennmann, Eva, Schneider, Nadine, Lange, Gudrun, Rarey, Matthias

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

58

Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach

Kumar, Ashutosh, Ito, Akihiro, Hirohama, Mikako, Yoshida, Minoru, Zhang, Kam YJ

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

59

Accelerating turbo similarity searching in chemoinformatics on multicore and GPU platforms

Al Laila, Marwah, Malim, Nurul, Rashid, Nur’Aini

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

60

Computational evaluation of the η6-arene during the ATH of imines on Noyori’s RuII catalyst

Kacer, Petr, Petr, Sot, Pechacek, Jan, Januscak, Jakub, Kuzma, Marek

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

61

InChI – the worldwide chemical structure standard

Heller, Stephen

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

62

Dualsteric modulators of the M2 muscarinic acetylcholine receptor

Bermudez, Marcel, Wolber, Gerhard

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

63

Consistency of sugar structures and their annotation in the PDB

Jaiswal, Deepti, Sehnal, David, Vařeková, Radka, Ionescu, Crina-Maria, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

64

Towards understanding the chemical environment effect on gold-containing clusters

Mollenhauer, Doreen, Gaston, Nicola

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

65

Exploiting solvent effects in drug design and optimization

Truchon, Jean-Francois, Grabowski, Kristina, Sander, Barbara, Ajamian, Alain

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

66

Fuzzy context specific matched molecular pairs

Schmidtke, Peter, le Guilloux, Vincent

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 71 KB

english, 2014

67

A new method for rapid comparison of protein binding pockets by capturing spatial distributions

Krotzky, Timo, Klebe, Gerhard

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

68

Peptide lineup against Gram-negative bacterial infection – first-in-class peptide inhibitor of H. pylori HtrA

Perna, Anna M, Schmidt, Thomas, Fugmann, Tim, Tegtmeyer, Nicole, Backert, Steffen, Wessler, Silja, Schneider, G

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

69

Target prediction by cascaded self-organizing maps for ligand de-orphaning and side-effect investigation

Reker, Daniel, Rodrigues, Tiago, Schneider, Petra, Schneider, Gisbert

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

70

Targeting flexibility: a structure-based computational study revealing allosteric HIV-1 protease inhibitors

Kunze, Jens, Todoroff, Nickolay, Rodrigues, Tiago, Schneider, Petra, Schneider, Gisbert

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 66 KB

english, 2014

71

Go with the flow: de-orphaning focused combinatorial libraries

Reutlinger, Michael, Rodrigues, Tiago, Schneider, Petra, Schneider, Gisbert

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 68 KB

english, 2014

72

Compound optimization through data set-dependent chemical transformations

de León, Antonio, Bajorath, Jürgen

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

73

Discovery of novel α-amylase inhibitors using structure-based drug design

Al-Asri, Jamil, Wolber, Gerhard

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 283 KB

english, 2014

74

ChemicalToolBoX and its application on the study of the drug like and purchasable space

Lucas, Xavier, Grüning, Björn A, Günther, Stefan

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 100 KB

english, 2014

75

Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web

Stierand, Katrin, Harder, Tim, Wissler, Lothar, Lemmen, Christian, Rarey, Matthias

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

76

Parameterization to NDDO-based polarizable force field

Thomas, Heike, Hennemann, Matthias, Guessregen, Stefan, Clark, Timothy

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 71 KB

english, 2014

77

Pharmacophore annotation using extended Hückel theory

Labute, Paul, Kossner, Markus, Ajamian, Alain, Santavy, Martin, Lin, Anna

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

78

Surflex-QMOD: physically meaningful QSAR

Steudle, Alexander, Varela, Rocco, Jain, Ajay N

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 58 KB

english, 2014

79

Is there a sodium effect in fibrillar amyloid-β oligomers?

Horn, Anselm HC, Huraskin, Danyil, Sticht, Heinrich

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 75 KB

english, 2014

80

SiteHopper - a unique tool for binding site comparison

Batista, Jose, Hawkins, Paul CD, Tolbert, Robert, Geballe, Matthew T

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

81

Theoretical illustration of the effect of 1-ethyl-pyridinium trifluoroacetate ionic liquid in the enhancement of the Diels–Alder reaction of isoprene with acrylic acid

Chemouri, Hafida, Mekelleche, Sidi

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 95 KB

english, 2014

82

The application of statistical methods to cognate docking: A path forward?

Stahl, Gunther, Hawkins, Paul CD, McGann, Mark, Geballe, Matthew T, Warren, Gregory L

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

83

Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases

Cappel, Daniel, Myrianthopoulos, Vassilios, Mikros, Emmanuel, Sherman, Woody

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

84

Empirical charges for chemoinformatics applications

Bouchal, Tomáš, Vařeková, Radka, Raček, Tomáš, Ionescu, Crina-Maria, Geidl, Stanislav, Křenek, Aleš, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

85

QM quality atomic charges for proteins

Geidl, Stanislav, Ionescu, Crina-Maria, Vařeková, Radka, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

86

IterTunnel; a method for predicting and evaluating ligand EgressTunnels in proteins with buried active sites

Kingsley, Laura J, Lill, Markus A

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 70 KB

english, 2014

87

Charge-related topological index – various chemoinformatics applications

Kochev, Nikolay T, Bangov, Ivan, Petrov, Emil, Moskovkina, Marina, Stoyanov, Borislav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

88

The integration of Open3DTOOLS into the RDKit and KNIME

Tosco, Paolo, Stiefl, Nikolaus, Landrum, Greg

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 75 KB

english, 2014

89

Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

Truszkowski, Andreas, Fiethen, Annamaria, Kuhn, Hubert, Wiebringhaus, Thomas, Zielesny, Achim, Epple, Matthias

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 262 KB

english, 2014

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