Volume 47; Issue 4

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Journal of Chemical Information and Modeling
Volume 47; Issue 4

Journal of Chemical Information and Modeling

Volume 47; Issue 4

1

Chemoinformatic Analysis of NCI Preclinical Tumor Data: Evaluating Compound Efficacy from Mouse Xenograft Data, NCI-60 Screening Data, and Compound Descriptors

Wallqvist, Anders, Huang, Ruili, Covell, David G.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 523 KB

english, 2007

2

Comparison of Topological, Shape, and Docking Methods in Virtual Screening

McGaughey, Georgia B., Sheridan, Robert P., Bayly, Christopher I., Culberson, J. Chris, Kreatsoulas, Constantine, Lindsley, Stacey, Maiorov, Vladimir, Truchon, Jean-Francois, Cornell, Wendy D.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 477 KB

english, 2007

3

Evaluations of Molecular Docking Programs for Virtual Screening

Onodera, Kenji, Satou, Kazuhito, Hirota, Hiroshi

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 211 KB

english, 2007

4

Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods

Bertaccini, Edward J., Trudell, James R., Lindahl, Erik

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 767 KB

english, 2007

5

Ligand-Based Models for the Isoform Specificity of Cytochrome P450 3A4, 2D6, and 2C9 Substrates

Terfloth, Lothar, Bienfait, Bruno, Gasteiger, Johann

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 153 KB

english, 2007

6

Pose Prediction Accuracy in Docking Studies and Enrichment of Actives in the Active Site of GSK-3β

Gadakar, Pravin Kumar, Phukan, Samiron, Balaji, V. N.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 589 KB

english, 2007

7

Recent Advances in Chemoinformatics

Agrafiotis, Dimitris K., Bandyopadhyay, Deepak, Wegner, Jörg K., van Vlijmen, Herman

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 125 KB

english, 2007

8

Benchmarking of QSAR Models for Blood-Brain Barrier Permeation

Konovalov, Dmitry A., Coomans, Danny, Deconinck, Eric, Vander Heyden, Yvan

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 164 KB

english, 2007

9

GPCR Structure-Based Virtual Screening Approach for CB2 Antagonist Search

Chen, Jian-Zhong, Wang, Junmei, Xie, Xiang-Qun

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 1018 KB

english, 2007

10

Virtual Screening Studies to Design Potent CDK2-Cyclin A Inhibitors

Vadivelan, S., Sinha, Barij Nayan, Irudayam, Sheeba Jem, Jagarlapudi, Sarma A. R. P.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 492 KB

english, 2007

11

DNA Minor Groove Pharmacophores Describing Sequence Specific Properties

Spitzer, Gudrun M., Wellenzohn, Bernd, Laggner, Christian, Langer, Thierry, Liedl, Klaus R.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 681 KB

english, 2007

12

Consensus QSAR Models: Do the Benefits Outweigh the Complexity?

Hewitt, Mark, Cronin, Mark T. D., Madden, Judith C., Rowe, Philip H., Johnson, Clara, Obi, Anrdrea, Enoch, Steven J.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 284 KB

english, 2007

13

Identifying P-Glycoprotein Substrates Using a Support Vector Machine Optimized by a Particle Swarm

Huang, Jianping, Ma, Guangli, Muhammad, Ishtiaq, Cheng, Yiyu

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 131 KB

english, 2007

14

ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 2. Equations of State on Demand and Dynamic Updates over the Web

Diky, Vladimir, Muzny, Chris D., Lemmon, Eric W., Chirico, Robert D., Frenkel, Michael

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 381 KB

english, 2007

15

Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis

Wang, Junmei, Krudy, George, Hou, Tingjun, Zhang, Wei, Holland, George, Xu, Xiaojie

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 388 KB

english, 2007

16

Library Fingerprints: A Novel Approach to the Screening of Virtual Libraries

Klon, Anthony E., Diller, David J.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 332 KB

english, 2007

17

Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways

Oh, Mina, Yamada, Takuji, Hattori, Masahiro, Goto, Susumu, Kanehisa, Minoru

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 493 KB

english, 2007

18

Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems

Forli, Stefano, Botta, Maurizio

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 281 KB

english, 2007

19

Radial Basis Function Network-Based Transform for a Nonlinear Support Vector Machine as Optimized by a Particle Swarm Optimization Algorithm with Application to QSAR Studies

Tang, Li-Juan, Zhou, Yan-Ping, Jiang, Jian-Hui, Zou, Hong-Yan, Wu, Hai-Long, Shen, Guo-Li, Yu, Ru-Qin

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 115 KB

english, 2007

20

Learning Vector Quantization for Multiclass Classification: Application to Characterization of Plastics

Lloyd, Gavin R., Brereton, Richard G., Faria, Rita, Duncan, John C.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 246 KB

english, 2007

21

Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data

Crisman, Thomas J., Parker, Christian N., Jenkins, Jeremy L., Scheiber, Josef, Thoma, Mathis, Kang, Zhao Bin, Kim, Richard, Bender, Andreas, Nettles, James H., Davies, John W., Glick, Meir

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 438 KB

english, 2007

22

Rapid Estimation of Relative Protein−Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA

Brown, Scott P., Muchmore, Steven W.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 482 KB

english, 2007

23

Novel Virtual Screening Protocol Based on the Combined Use of Molecular Modeling and Electron-Ion Interaction Potential Techniques To Design HIV-1 Integrase Inhibitors

Tintori, Cristina, Manetti, Fabrizio, Veljkovic, Nevena, Perovic, Vladimir, Vercammen, Jo, Hayes, Sean, Massa, Silvio, Witvrouw, Myriam, Debyser, Zeger, Veljkovic, Veljko, Botta, Maurizio

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 299 KB

english, 2007

24

A Protein Folding Degree Measure and Its Dependence on Crystal Packing, Protein Size, Secondary Structure, and Domain Structural Class [ J. Chem. Inf. Comput. Sci. 44, 1238−1250 (2004)]

Journal:

Journal of Chemical Information and Modeling

Year:

2007

File:

PDF, 14 KB

2007

25

Unbiasing Scoring Functions: A New Normalization and Rescoring Strategy

Carta, Giorgio, Knox, Andrew J. S., Lloyd, David G.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 657 KB

english, 2007

26

Automatic Perception of Organic Molecules Based on Essential Structural Information

Zhao, Yuan, Cheng, Tiejun, Wang, Renxiao

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 117 KB

english, 2007

27

Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets

Zhou, Zhiyong, Felts, Anthony K., Friesner, Richard A., Levy, Ronald M.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 509 KB

english, 2007

28

Counting Clusters Using R -NN Curves

Guha, Rajarshi, Dutta, Debojyoti, Wild, David J., Chen, Ting

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 208 KB

english, 2007

29

Automated Pharmacophore Query Optimization with Genetic AlgorithmsA Case Study Using the MC4R System

Jia, Lei, Zou, Jinming, So, Sung-Sau, Sun, Hongmao

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 575 KB

english, 2007

30

Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study

Czodrowski, Paul, Sotriffer, Christoph A., Klebe, Gerhard

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 216 KB

english, 2007

31

A Multivariate Approach to Investigate Docking Parameters' Effects on Docking Performance

Andersson, C. David, Thysell, Elin, Lindström, Anton, Bylesjö, Max, Raubacher, Florian, Linusson, Anna

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 739 KB

english, 2007

32

Mining of Randomly Generated Molecular Fragment Populations Uncovers Activity-Specific Fragment Hierarchies

Batista, José, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 491 KB

english, 2007

33

Mechanism of the Kolbe−Schmitt Reaction. Structure of the Intermediate Potassium Phenoxide−CO 2 Complex

Marković, Zoran, Marković, Svetlana, Manojlović, Nedeljko, Predojević-Simović, Jasmina

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 213 KB

english, 2007

34

GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes

Tietze, Simon, Apostolakis, Joannis

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 1018 KB

english, 2007

35

Molecular Basis SetsA General Similarity-Based Approach for Representing Chemical Spaces

Raghavendra, Akshay S., Maggiora, Gerald M.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 185 KB

english, 2007

36

Large-Scale Annotation of Small-Molecule Libraries Using Public Databases

Zhou, Yingyao, Zhou, Bin, Chen, Kaisheng, Yan, S. Frank, King, Frederick J., Jiang, Shumei, Winzeler, Elizabeth A.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 286 KB

english, 2007

37

SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering

Fischer, J. Robert, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 896 KB

english, 2007

38

Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space

Borodina, Yulia V., Bolton, Evan, Fontaine, Fabien, Bryant, Stephen H.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 633 KB

english, 2007

39

Web Service Infrastructure for Chemoinformatics

Dong, Xiao, Gilbert, Kevin E., Guha, Rajarshi, Heiland, Randy, Kim, Jungkee, Pierce, Marlon E., Fox, Geoffrey C., Wild, David J.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 317 KB

english, 2007

40

Recursive Distance Partitioning Algorithm for Common Pharmacophore Identification

Zhu, Fangqiang, Agrafiotis, Dimitris K.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 136 KB

english, 2007

41

A Database of Historically-Observed Chemical Replacements

Haubertin, David Y., Bruneau, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 322 KB

english, 2007

42

Modeling Robust QSAR 3: SOM-4D-QSAR with Iterative Variable Elimination IVE-PLS: Application to Steroid, Azo Dye, and Benzoic Acid Series

Bak, Andrzej, Polanski, Jaroslaw

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 784 KB

english, 2007

43

Exploring Peptide-likeness of Active Molecules Using 2D Fingerprint Methods

Eckert, Hanna, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 1.06 MB

english, 2007

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