Volume 53; Issue 5

Main
Journal of Chemical Information and Modeling
Volume 53; Issue 5

Journal of Chemical Information and Modeling

Volume 53; Issue 5

1

Molecular Dynamics Simulations of the Adenosine A2a Receptor: Structural Stability, Sampling, and Convergence

Ng, Hui Wen, Laughton, Charles A., Doughty, Stephen W.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.24 MB

english, 2013

2

Reaction Schemes Visualized in Network Form: The Syntheses of Strychnine as an Example

Proudfoot, John R.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.61 MB

english, 2013

3

Hit Expansion Approaches Using Multiple Similarity Methods and Virtualized Query Structures

Bergner, Andreas, Parel, Serge P.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 703 KB

english, 2013

4

Compound Pathway Model To Capture SAR Progression: Comparison of Activity Cliff-Dependent and -Independent Pathways

Stumpfe, Dagmar, Dimova, Dilyana, Heikamp, Kathrin, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 821 KB

english, 2013

5

Fighting Obesity with a Sugar-Based Library: Discovery of Novel MCH-1R Antagonists by a New Computational–VAST Approach for Exploration of GPCR Binding Sites

Heifetz, Alexander, Barker, Oliver, Verquin, Geraldine, Wimmer, Norbert, Meutermans, Wim, Pal, Sandeep, Law, Richard J., Whittaker, Mark

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.75 MB

english, 2013

6

Identification of Compounds with Potential Antibacterial Activity against Mycobacterium through Structure-Based Drug Screening

Kinjo, Tomohiro, Koseki, Yuji, Kobayashi, Maiko, Yamada, Atsumi, Morita, Koji, Yamaguchi, Kento, Tsurusawa, Ryoya, Gulten, Gulcin, Komatsu, Hideyuki, Sakamoto, Hiroshi, Sacchettini, James C., Kitamura

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 2.13 MB

english, 2013

7

Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL

Makarewicz, Tomasz, Kaźmierkiewicz, Rajmund

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 683 KB

english, 2013

8

Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance

Karaboga, Arnaud S., Planesas, Jesús M., Petronin, Florent, Teixidó, Jordi, Souchet, Michel, Pérez-Nueno, Violeta I.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 2.36 MB

english, 2013

9

Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling

Cui, Wei, Cheng, Yuan-Hua, Geng, Ling-Ling, Liang, Den-Sheng, Hou, Ting-Jun, Ji, Ming-Juan

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 2.47 MB

english, 2013

10

Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures

Ding, Bo, Li, Nan, Wang, Wei

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 3.08 MB

english, 2013

11

Determination of Toxicant Mode of Action by Augmented Top Priority Fragment Class

Casalegno, Mosé, Sello, Guido

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 595 KB

english, 2013

12

Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields

Dahlgren, Markus K., Schyman, Patric, Tirado-Rives, Julian, Jorgensen, William L.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 638 KB

english, 2013

13

ChemCalc: A Building Block for Tomorrow’s Chemical Infrastructure

Patiny, Luc, Borel, Alain

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 513 KB

english, 2013

14

TRAPP: A Tool for Analysis of Tra nsient Binding P ockets in P roteins

Kokh, Daria B., Richter, Stefan, Henrich, Stefan, Czodrowski, Paul, Rippmann, Friedrich, Wade, Rebecca C.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 3.45 MB

english, 2013

15

Identification of a New Binding Site in E. coli FabH using Molecular Dynamics Simulations: Validation by Computational Alanine Mutagenesis and Docking Studies

Ramamoorthy, Divya, Turos, Edward, Guida, Wayne C.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 3.70 MB

english, 2013

16

Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitors

Langdon, Sarah R., Westwood, Isaac M., van Montfort, Rob L. M., Brown, Nathan, Blagg, Julian

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 3.70 MB

english, 2013

17

Similarity Boosted Quantitative Structure–Activity Relationship—A Systematic Study of Enhancing Structural Descriptors by Molecular Similarity

Girschick, Tobias, Almeida, Pedro R., Kramer, Stefan, Stålring, Jonna

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 851 KB

english, 2013

18

Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide

Mallajosyula, Sairam S., Adams, Kristie M., Barchi, Joseph J., MacKerell, Alexander D.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.69 MB

english, 2013

19

Exploring the Potential of Protein-Based Pharmacophore Models in Ligand Pose Prediction and Ranking

Hu, Bingjie, Lill, Markus A.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

20

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions

Zheng, Zheng, Merz, Kenneth M.

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 4.43 MB

english, 2013

21

Consensus Methods for Combining Multiple Clusterings of Chemical Structures

Saeed, Faisal, Salim, Naomie, Abdo, Ammar

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.46 MB

english, 2013

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