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793 Newest Publications in journal of chemical information and modeling
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CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
10-05-2013 | Kelly L. Damm-Ganamet; Richard D. Smith; James B. Dunbar, Jr.; Jeanne A. Stuckey; Heather A. Carlson, Journal of Chemical Information and Modeling, 2013
The Community Structure–Activity Resource (CSAR) recently held its first blinded exercise based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann Arbor. A total of 20 research groups submitted results for the benchmark exercise where the goal was to compare ...
CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys
10-05-2013 | James B. Dunbar, Jr.; Richard D. Smith; Kelly L. Damm-Ganamet; Aqeel Ahmed; Emilio Xavier Esposito; James Delpropost ..., Journal of Chemical Information and Modeling, 2013
A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has currently ...
Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise
08-05-2013 | Ashutosh Kumar; Kam Y. J. Zhang, Journal of Chemical Information and Modeling, 2013
Water molecules are routinely included in molecular docking methods and protocols because of their important role in mediating ligand protein interactions. However, it is still unclear that the inclusion of explicit water molecules improves docking accuracy. To explore the effect of including ...
Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL
06-05-2013 | Tomasz Makarewicz; Rajmund Kaźmierkiewicz, Journal of Chemical Information and Modeling, 2013
The molecular models stored as PDB formatted files are static, but most of the biomolecular systems display a dynamic behavior, in other words their conformations depend on time. To get the dynamic model from the static one, one needs to perform the molecular dynamics (MD) simulation using ...
Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures
30-04-2013 | Bo Ding; Nan Li; Wei Wang, Journal of Chemical Information and Modeling, 2013
Drug resistance severely erodes the efficacy of therapeutic treatments for many diseases. Assessing the potency of a drug lead to combat resistance is no doubt critical for designing new drugs or new therapeutic combinations. Virtual screening is often the first step in drug discovery and a ...
Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program
30-04-2013 | Claudia Beato; Andrea R. Beccari; Carlo Cavazzoni; Simone Lorenzi; Gabriele Costantino, Journal of Chemical Information and Modeling, 2013
On route toward a novel de novo design program, called LiGen, we developed a docking program, LiGenDock, based on pharmacophore models of binding sites, including a non-enumerative docking algorithm. In this paper, we present the functionalities of LiGenDock and its accompanying module ...
ChemCalc: A Building Block for Tomorrow’s Chemical Infrastructure
30-04-2013 | Luc Patiny; Alain Borel, Journal of Chemical Information and Modeling, 2013
Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data ...
Similarity Boosted Quantitative Structure–Activity Relationship—A Systematic Study of Enhancing Structural Descriptors by Molecular Similarity
29-04-2013 | Tobias Girschick; Pedro R. Almeida; Stefan Kramer; Jonna Stålring, Journal of Chemical Information and Modeling, 2013
The concept of molecular similarity is one of the most central in the fields of predictive toxicology and quantitative structure–activity relationship (QSAR) research. Many toxicological responses result from a multimechanistic process and, consequently, structural diversity among the active ...
Consensus Methods for Combining Multiple Clusterings of Chemical Structures
26-04-2013 | Faisal Saeed; Naomie Salim; Ammar Abdo, Journal of Chemical Information and Modeling, 2013
The goal of consensus clustering methods is to find a consensus partition that optimally summarizes an ensemble and improves the quality of clustering compared with single clustering algorithms. In this paper, an enhanced voting-based consensus method was introduced and compared with other ...
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
26-04-2013 | Alexander Heifetz; Oliver Barker; Geraldine Verquin; Norbert Wimmer; Wim Meutermans; Sandeep Pal; Richard J. Law; Ma ..., Journal of Chemical Information and Modeling, 2013
Obesity is an increasingly common disease. While antagonism of the melanin-concentrating hormone-1 receptor (MCH-1R) has been widely reported as a promising therapeutic avenue for obesity treatment, no MCH-1R antagonists have reached the market. Discovery and optimization of new chemical ...
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