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Latent Semantic Structure Indexing
Latent semantic structure indexing (LaSSI) is a technique for calculating chemical similarity derived from latent semantic analysis (LSA). LaSSI was developed at Merck & Co. and patented in 2007 by Richard Hull, Eugene Fluder, Suresh Singh, Robert Sheridan, Robert Nachbar and Simon Kearsley. Overview LaSSI is similar to LSA in that it involves the construction of an occurrence matrix from a corpus of items and the application of singular value decomposition to that matrix to derive latent features. What differs is that the occurrence matrix represents the frequency of two- and three-dimensional chemical descriptors (rather than natural language terms) found within a chemical database of chemical structures. This process derives latent chemical structure concepts that can be used to calculate chemical similarities and structure–activity relationships for drug discovery In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Latent Semantic Analysis
Latent semantic analysis (LSA) is a technique in natural language processing, in particular distributional semantics, of analyzing relationships between a set of documents and the terms they contain by producing a set of concepts related to the documents and terms. LSA assumes that words that are close in meaning will occur in similar pieces of text (the distributional hypothesis). A matrix containing word counts per document (rows represent unique words and columns represent each document) is constructed from a large piece of text and a mathematical technique called singular value decomposition (SVD) is used to reduce the number of rows while preserving the similarity structure among columns. Documents are then compared by cosine similarity between any two columns. Values close to 1 represent very similar documents while values close to 0 represent very dissimilar documents. An information retrieval technique using latent semantic structure was patented in 1988US Patent 4,839 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Merck & Co
Merck & Co., Inc. is an American multinational pharmaceutical company headquartered in Rahway, New Jersey, and is named for Merck Group, founded in Germany in 1668, of whom it was once the American arm. The company does business as Merck Sharp & Dohme or MSD outside the United States and Canada. Merck & Co. was originally established as the American affiliate of Merck Group in 1891. Merck develops and produces medicines, vaccines, biologic therapies and animal health products. It has multiple blockbuster drugs or products each with 2020 revenues including cancer immunotherapy, anti-diabetic medication and vaccines against HPV and chickenpox. The company is ranked 71st on the 2022 ''Fortune'' 500 and 87th on the 2022 ''Forbes'' Global 2000, both based on 2021 revenues. Products The company develops medicines, vaccines, biologic therapies and animal health products. In 2020, the company had 6 blockbuster drugs or products, each with over $1 billion in revenue: ''Keytrud ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Singular Value Decomposition
In linear algebra, the singular value decomposition (SVD) is a factorization of a real or complex matrix. It generalizes the eigendecomposition of a square normal matrix with an orthonormal eigenbasis to any \ m \times n\ matrix. It is related to the polar decomposition. Specifically, the singular value decomposition of an \ m \times n\ complex matrix is a factorization of the form \ \mathbf = \mathbf\ , where is an \ m \times m\ complex unitary matrix, \ \mathbf\ is an \ m \times n\ rectangular diagonal matrix with non-negative real numbers on the diagonal, is an n \times n complex unitary matrix, and \ \mathbf\ is the conjugate transpose of . Such decomposition always exists for any complex matrix. If is real, then and can be guaranteed to be real orthogonal matrices; in such contexts, the SVD is often denoted \ \mathbf^\mathsf\ . The diagonal entries \ \sigma_i = \Sigma_\ of \ \mathbf\ are uniquely determined by and are known as the singular values ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Database
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data. Types of chemical databases Bioactivity database Bioactivity databases correlate structures or other chemical information to bioactivity results taken from bioassays in literature, patents, and screening programs. Chemical structures Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D structural formulae). While these are ideal visual representations for the chemist, they are unsuitable for computational use and especially for search and storage. Small molecules (also called ligands in drug design applications), are usually represented using lists of atoms and their connections. Large molecules such as proteins are however more compactly represented using the sequences of their amino acid bui ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structure–activity Relationship
The structure–activity relationship (SAR) is the relationship between the chemical structure of a molecule and its biological activity. This idea was first presented by Crum-Brown and Fraser in 1865. The analysis of SAR enables the determination of the chemical group responsible for evoking a target biological effect in the organism. This allows modification of the effect or the potency of a bioactive compound (typically a drug) by changing its chemical structure. Medicinal chemists use the techniques of chemical synthesis to insert new chemical groups into the biomedical compound and test the modifications for their biological effects. This method was refined to build mathematical relationships between the chemical structure and the biological activity, known as quantitative structure–activity relationships (QSAR). A related term is structure affinity relationship (SAFIR). Structure-biodegradability relationship The large number of synthetic organic chemicals currently in p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Drug Discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate medications are discovered. Historically, drugs were discovered by identifying the active ingredient from traditional remedies or by serendipitous discovery, as with penicillin. More recently, chemical libraries of synthetic small molecules, natural products or extracts were screened in intact cells or whole organisms to identify substances that had a desirable therapeutic effect in a process known as classical pharmacology. After sequencing of the human genome allowed rapid cloning and synthesis of large quantities of purified proteins, it has become common practice to use high throughput screening of large compounds libraries against isolated biological targets which are hypothesized to be disease-modifying in a process known as reverse pharmacology. Hits from these screens are then tested in cells and then in animals for efficacy. Modern drug discovery i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cheminformatics
Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such ''in silico'' techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied. History Cheminformatics has been an active field in various guises since the 1970s and earlier, with activity in academic departments and commercial pharmaceutical research and de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
