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The early drug discovery phase in pharmaceutical research and development marks the beginning of a long, complex and costly process of bringing a new molecular entity to market. As such, it plays a critical ro...
In this work, we analyzed and compared the distribution profiles of a wide variety of molecular properties for three compound classes: drug-like compounds in MDL Drug Data Report (MDDR), non-drug-like compound...
Relating chemical features to bioactivities is critical in molecular design and is used extensively in the lead discovery and optimization process. A variety of techniques from statistics, data mining and mach...
To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D) descriptions to the small-...
Ligand-based virtual screening using molecular shape is an important tool for researchers who wish to find novel chemical scaffolds in compound libraries. The Ultrafast Shape Recognition (USR) algorithm is cap...
Assigning bond orders is a necessary and essential step for characterizing a chemical structure correctly in force field based simulations. Several methods have been developed to do this. They all have advanta...
HSQC spectra are routinely acquired for chemical structure analysis based on hydrogen and carbon chemical environments. Two fast HSQC peak matching algorithms have been developed; a nearest neighbour approach ...
Displaying chemical structures in LATE X documents currently requires either hand-coding of the structures using one of several LATE X packages, or the inclusion of finished graphics files produced with an ext...
A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-gr...
There are two line notations of chemical structures that have established themselves in the field: the SMILES string and the InChI string. The InChI aims to provide a unique, or canonical, identifier for chemi...
Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Gen...
High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screen...
Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked activel...
With the exponential increase in the number of available ligand-receptor complexes, researchers are becoming more dedicated to mine these complexes to facilitate the drug design and development process. Theref...
The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related area...
MicroRNAs (miRNA) are small endogenously transcribed regulatory RNA which modulates gene expression at a post transcriptional level. These small RNAs have now been shown to be critical regulators in a number o...
This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (C...
The articles in this special issue arise from a workshop and symposium held in January 2012 (Semantic Physical Science’). We invited people who shared our vision for the potential of the web to support chemica...
Searching for substructures in molecules belongs to the most elementary tasks in cheminformatics and is nowadays part of virtually every cheminformatics software. The underlying algorithms, used over several d...
Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to...
Small molecule chemistry is of central importance to a number of R&D companies in diverse areas such as the pharmaceutical, nutraceutical, food flavoring, and cosmeceutical industries. In order to store and ma...
Experimental screening of chemical compounds for biological activity is a time consuming and expensive practice. In silico predictive models permit inexpensive, rapid “virtual screening” to prioritize selection o...
Terms representing chemical concepts found the Unified Medical Language System (UMLS) are used to derive an expanded semantic network with mutually exclusive semantic types. The UMLS Semantic Network (SN) is c...
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
This article is part of a Supplement: Volume 4 Supplement 1
