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This article is part of a Supplement: Volume 3 Supplement 1
This article is part of a Supplement: Volume 3 Supplement 1
This article is part of a Supplement: Volume 3 Supplement 1
Model-based virtual screening plays an important role in the early drug discovery stage. The outcomes of high-throughput screenings are a valuable source for machine learning algorithms to infer such models. B...
The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.
Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-ene...
Standard approaches to address the performance of predictive models that used common statistical measurements for the entire data set provide an overview of the average performance of the models across the ent...
So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure edit...
In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure...
PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemica...
The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints...
The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex m...
CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and ...
We collected data from over 80 different cytotoxicity assays from Pfizer in-house work as well as from public sources and investigated the feasibility of using these datasets, which come from a variety of assa...
Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clu...
Metabolomics experiments involve generating and comparing small molecule (metabolite) profiles from complex mixture samples to identify those metabolites that are modulated in altered states (e.g., disease, dr...
A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates ...
OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical...
In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to ...
QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, bu...
The original article was published in Journal of Cheminformatics 2010 2:3
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
