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An increasing number of researchers are focused on strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs.
The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from...
Natural products are considered a rich source of new chemical structures that may lead to the therapeutic agents in all major disease areas. About 50% of the drugs introduced in the market in the last 20 years...
While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources enhance crawli...
One of the main topics in the development of quantitative structure-property relationship (QSPR) predictive models is the identification of the subset of variables that represent the structure of a molecule an...
Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular r...
Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the ext...
This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of ...
In order to better understand the structural features of natural compounds from traditional Chinese medicines, the scaffold architectures of drug-like compounds in MACCS-II Drug Data Report (MDDR), non-drug-li...
The Online Chemical Modeling Environment (OCHEM, http://ochem.eu) is a web-based platform that provides tools for automation of typical steps necessary to create a...
UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based ...
Mycobacterium tuberculosis encodes 11 putative serine-threonine proteins Kinases (STPK) which regulates transcription, cell development and interaction with the host cells. From the 11 STPKs three kinases name...
PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived...
Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound ...
InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of I...
Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in ...
Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few...
Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as quantitative structure–property relationships modell...
Exchange of chemical structures between practicing chemists is essential to chemical communication. The International Chemical Identifier (InChI) provides a means for lossless communication of structures witho...
The International Chemical Identifier (InChI) has had a dramatic impact on providing a means by which to deduplicate, validate and link together chemical compounds and related information across databases. Its...
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
