Page 20 of 30
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
In the European Union, medicines are authorised for some rare disease only if they are judged to be dissimilar to authorised orphan drugs for that disease. This paper describes the use of 2D fingerprints to sh...
Few environments have been developed or deployed to widely share biomolecular simulation data or to enable collaborative networks to facilitate data exploration and reuse. As the amount and complexity of data ...
The Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings....
An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in ...
With the rapid development of high-throughput genomic technologies and the accumulation of genome-wide datasets for gene expression profiling and biological networks, the impact of diseases and drugs on gene e...
In order to exploit the vast body of currently inaccessible chemical information held in Electronic Laboratory Notebooks (ELNs) it is necessary not only to make it available but also to develop protocols for d...
Cardiovascular disease (CVD) is the leading cause of death and associates with multiple risk factors. Herb medicines have been used to treat CVD long ago in china and several natural products or derivatives (e...
Virtual screening in the form of similarity rankings is often applied in the early drug discovery process to rank and prioritize compounds from a database. This similarity ranking can be achieved with structur...
‘Phylogenetic trees’ are commonly used for the analysis of chemogenomics datasets and to relate protein targets to each other, based on the (shared) bioactivities of their ligands. However, no real assessment ...
Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical struc...
Multiple validation techniques (Y-scrambling, complete training/test set randomization, determination of the dependence of R2test on the number of randomization cycles, etc.) aimed to improve the reliability of t...
While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason...
The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique text descript...
To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribu...
Fingerprint similarity is a common method for comparing chemical structures. Similarity is an appealing approach because, with many fingerprint types, it provides intuitive results: a chemist looking at two mo...
While a large body of work exists on comparing and benchmarking descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 amino a...
While a large body of work exists on comparing and benchmarking of descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 diff...
2D diagrams are widely used in the scientific literature to represent interactions between ligands and biomacromolecules. Such schematic diagrams are very helpful to better understand the chemical interactions...
Working with small‐molecule datasets is a routine task forcheminformaticians and chemists. The analysis and comparison of vendorcatalogues and the compilation of promising candidates as starting pointsfor scre...
In the last decade the standard Naive Bayes (SNB) algorithm has been widely employed in multi–class classification problems in cheminformatics. This popularity is mainly due to the fact that the algorithm is s...
Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.
Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom co...
The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many...
The rapid access to intrinsic physicochemical properties of molecules is highly desired for large scale chemical data mining explorations such as mass spectrum prediction in metabolomics, toxicity risk assessm...
A plethora of studies indicate that the development of multi-target drugs is beneficial for complex diseases like cancer. Accurate QSAR models for each of the desired targets assist the optimization of a lead ...
The World Anti-Doping Agency (WADA) publishes the Prohibited List, a manually compiled international standard of substances and methods prohibited in-competition, out-of-competition and in particular sports. I...
Existing computational methods for drug repositioning either rely only on the gene expression response of cell lines after treatment, or on drug-to-disease relationships, merging several information levels. Ho...
Herbal medicine has long been viewed as a valuable asset for potential new drug discovery and herbal ingredients’ metabolites, especially the in vivo metabolites were often found to gain better pharmacological, p...
With the growing popularity of using QSAR predictions towards regulatory purposes, such predictive models are now required to be strictly validated, an essential feature of which is to have the model’s Applica...
Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening. A huge variety of fingerprints exist and their performance, usually assessed in retrospective be...
Multidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinf...
A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser ...
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Un...
Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the ...
A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from t...
Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 m...
There is a growing body of literature describing the properties of marketed drugs, the concept of drug-likeness and the vastness of chemical space. In that context, enumerative combinatorics with simple atomic...
