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BindingDB
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. As of March, 2011, BindingDB contains about 650,000 binding data, for 5,700 protein targets and 280,000 small molecules. BindingDB also includes a small collection of host–guest binding data of interest to chemists studying supramolecular systems. The purpose of BindingDB is to support medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modelling approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of molecular recognition. The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isother ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PubChem
PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains multiple substance descriptions and small molecules with fewer than 100 atoms and 1,000 bonds. More than 80 database vendors contribute to the growing PubChem database. History PubChem was released in 2004 as a component of the Molecular Libraries Program (MLP) of the NIH. As of November 2015, PubChem contains more than 150 million depositor-provided substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results (from over 1 million assay experiments performed on more t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SAMPL Challenge
SAMPL (Statistical Assessment of the Modeling of Proteins and Ligands) is a set of community-wide blind challenges aimed to advance computational techniques as standard predictive tools in rational drug design. A broad range of biologically relevant systems with different sizes and levels of complexities including proteins, host–guest complexes, and drug-like small molecules have been selected to test the latest modeling methods and force fields in SAMPL. New experimental data, such as binding affinity and hydration free energy, are withheld from participants until the prediction submission deadline, so that the true predictive power of methods can be revealed. The most recent SAMPL5 challenge contains two prediction categories: the binding affinity of host–guest systems, and the distribution coefficients of drug-like molecules between water and cyclohexane. Since 2008, the SAMPL challenge series has attracte interest from scientists engaged in the field of computer-aided dru ... [...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 buildin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Skaggs School Of Pharmacy And Pharmaceutical Sciences
The Skaggs School of Pharmacy and Pharmaceutical Sciences is a graduate-level pharmacy school at the University of California, San Diego. It offers five educational programs: *Doctor of Pharmacy (Pharm.D.) degree awarded in a four-year program *Joint Bachelor of Science (BS) in Chemistry and Pharm.D. degree awarded in a seven-year program in cooperation with UCSD's Department of Chemistry and Biochemistry *Ph.D. degree in pharmaceutical and biomedical sciences *Post Pharm.D. pharmacy practice and specialty residencies and research fellowships *A continuing education program for practicing pharmacists. Prior to the establishment of the school, San Diego was the largest metropolitan city in the USA without a local pharmacy school. History The Skaggs School was authorized by the Regents of the University of California The Regents of the University of California (also referred to as the Board of Regents to distinguish the board from the corporation it governs of the same na ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UC San Diego
The University of California, San Diego (UC San Diego or colloquially, UCSD) is a public university, public Land-grant university, land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the southernmost of the ten campuses of the University of California, and offers over 200 undergraduate and graduate degree programs, enrolling 33,096 undergraduate and 9,872 graduate students. The university occupies near the coast of the Pacific Ocean, with the main campus resting on approximately . UC San Diego is ranked among the best universities in the world by major college and university rankings. UC San Diego consists of twelve undergraduate, graduate and professional schools as well as seven undergraduate residential colleges. It received over 140,000 applications for undergraduate admissions in Fall 2021, making it the second most applied-to university in the United States. UC San Diego H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
N-ethylmaleimide Sensitive Fusion Protein
''N''-ethylmaleimide-sensitive factor, also known as NSF or ''N''-ethylmaleimide sensitive fusion proteins, is an enzyme which in humans is encoded by the ''NSF'' gene. Function NSF is a homohexameric AAA ATPase involved in membrane fusion. NSF is ubiquitously found in the membrane of eukaryotic cells. It is a central component of the cellular machinery in the transfer of membrane vesicles from one membrane compartment to another. During this process, SNARE proteins on two joining membranes (usually a vesicle and a target membrane such as the plasma membrane) form a complex, with the α-helical domains of the SNAREs coiling around each other and forming a very stable four-helix bundle. As SNAREs intertwine, they pull the vesicle towards the target membrane, excluding water and promoting fusion of the vesicle with the target membrane. NSF unravels SNARE complexes once membrane fusion has occurred, using the hydrolysis of ATP as an energy source, allowing the dissociated SNAREs ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NIST
The National Institute of Standards and Technology (NIST) is an agency of the United States Department of Commerce whose mission is to promote American innovation and industrial competitiveness. NIST's activities are organized into physical science laboratory programs that include nanoscale science and technology, engineering, information technology, neutron research, material measurement, and physical measurement. From 1901 to 1988, the agency was named the National Bureau of Standards. History Background The Articles of Confederation, ratified by the colonies in 1781, provided: The United States in Congress assembled shall also have the sole and exclusive right and power of regulating the alloy and value of coin struck by their own authority, or by that of the respective states—fixing the standards of weights and measures throughout the United States. Article 1, section 8, of the Constitution of the United States, ratified in 1789, granted these powers to the new Congre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChEMBL
ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK. The database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, led by John Overington. Scope and access The ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50. Data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 (ChEMBL_02) was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 com ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Recognition
The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, halogen bonding, or resonant interaction effects. In addition to these ''direct'' interactions, solvents can play a dominant ''indirect'' role in driving molecular recognition in solution. The host and guest involved in molecular recognition exhibit molecular complementarity. Exceptions are molecular containers, including e.g. nanotubes, in which portals essentially control selectivity. Biological systems Molecular recognition plays an important role in biological systems and is observed in between receptor-ligand, antigen-antibody, DNA-protein, sugar- lectin, RNA-ribosome, etc. An important example of molecular recognition is the antibiotic vancomycin that selectively binds with the peptides with terminal D-alanyl-D-alanine in bacterial cells ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Docking (molecular)
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced. Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target bind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
