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List Of Protein-ligand Docking Software
The number of notable protein-ligand docking programs currently available is high and has been steadily increasing over the last decades. The following list presents an overview of the most common notable programs, listed alphabetically, with indication of the corresponding year of publication, involved organisation or institution, short description, availability of a webservice and the license. This table is comprehensive but not complete. References External links * {{Chemistry software Structural bioinformatics software Molecular modelling software Computational chemistry software Lists of software ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein–ligand Docking
Protein–ligand docking is a molecular modelling technique. The goal of protein–ligand docking is to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme. Pharmaceutical research employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals in order to select likely drug candidates. There has been rapid development in computational ability to determine protein structure with programs such as AlphaFold, and the demand for the corresponding protein-ligand docking predictions is driving implementation of software that can find accurate models. Once the protein folding can be predicted accurately along with how the ligands of various structures will bind to the protein, the ability for drug development to progress at a much faster rate becomes possible. History Computer-aided drug design (CADD) was introduced in the 1980s in order to screen for nove ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RDock
rDock (previously RiboDock) is an open-source molecular docking software that be used for docking small molecules against proteins and nucleic acids. It is primarily designed for high-throughput virtual screening and prediction of binding mode. History The development of rDock started in 1998 in RiboTargets (later Vernalis (R&D) Ltd). The software was originally called RiboDock. The development went on until 2006 when the software was licensed to University of York for academic distribution and also maintenance. Six years later, in 2012, Vernalis and University of York decided to release rDock as open-source software to allow its further development by the wider community. The version that was released as open source is developed and supported by University of Barcelona on SourceForge. The development on SourceForge stalled after June 2014. A fork named RxDock is continuing the development of rDock since April 2019 on GitLab. As of April 2022, the RxDock project developmen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling Software
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not considere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Bioinformatics Software
A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as biological organisms, minerals and chemicals. Abstract structures include data structures in computer science and musical form. Types of structure include a hierarchy (a cascade of one-to-many relationships), a network featuring many-to-many links, or a lattice featuring connections between components that are neighbors in space. Load-bearing Buildings, aircraft, skeletons, anthills, beaver dams, bridges and salt domes are all examples of load-bearing structures. The results of construction are divided into buildings and non-building structures, and make up the infrastructure of a human society. Built structures are broadly divided by their varying design approaches and standards, into categories including building structur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Generalized Born
Implicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes. The implicit solvation model is justified in liquids, where the potential of mean force can be applied to approximate the averaged behavior of many highly dynamic solvent molecules. However, the interfaces and the interiors of biological membranes or proteins can also be considered as media with specific solvation or dielectric properties. These media are not necessarily uniform, since their properti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Zurich
The University of Zürich (UZH, german: Universität Zürich) is a public research university located in the city of Zürich, Switzerland. It is the largest university in Switzerland, with its 28,000 enrolled students. It was founded in 1833 from the existing colleges of theology, law, medicine which go back to 1525, and a new faculty of philosophy. Currently, the university has seven faculties: Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. The university offers the widest range of subjects and courses of any Swiss higher education institution. History The University of Zurich was founded on April 29, 1833, when the existing colleges of theology, the ''Carolinum'' founded by Huldrych Zwingli in 1525, law and medicine were merged with a new faculty of Philosophy. It was the first university in Europe to be founded by the state rather than a monarch or church. In the university's early years, the 183 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SEED
A seed is an embryonic plant enclosed in a protective outer covering, along with a food reserve. The formation of the seed is a part of the process of reproduction in seed plants, the spermatophytes, including the gymnosperm and angiosperm plants. Seeds are the product of the ripened ovule, after the embryo sac is fertilized by sperm from pollen, forming a zygote. The embryo within a seed develops from the zygote, and grows within the mother plant to a certain size before growth is halted. The seed coat arises from the integuments of the ovule. Seeds have been an important development in the reproduction and success of vegetable gymnosperm and angiosperm plants, relative to more primitive plants such as ferns, mosses and liverworts, which do not have seeds and use water-dependent means to propagate themselves. Seed plants now dominate biological niches on land, from forests to grasslands both in hot and cold climates. The term "seed" also has a general me ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU Lesser General Public License
The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate a software component released under the LGPL into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own components. However, any developer who modifies an LGPL-covered component is required to make their modified version available under the same LGPL license. For proprietary software, code under the LGPL is usually used in the form of a shared library, so that there is a clear separation between the proprietary and LGPL components. The LGPL is primarily used for software libraries, although it is also used by some stand-alone applications. The LGPL was developed as a compromise between the strong copyleft of the GNU General Public License (GPL) and more permissive licenses such as the BSD licenses and the MIT L ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virtual Screening
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme. Virtual screening has been defined as "automatically evaluating very large libraries of compounds" using computer programs. As this definition suggests, VS has largely been a numbers game focusing on how the enormous chemical space of over 1060 conceivable compounds can be filtered to a manageable number that can be synthesized, purchased, and tested. Although searching the entire chemical universe may be a theoretically interesting problem, more practical VS scenarios focus on designing and optimizing targeted combinatorial libraries and enriching libraries of available compounds from in-house compound repositories or vendor offerings. As the accuracy of the method has increased, virtual screening has become an integral part of the drug discove ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Barcelona
The University of Barcelona ( ca, Universitat de Barcelona, UB; ; es, link=no, Universidad de Barcelona) is a public university located in the city of Barcelona, Catalonia, in Spain. With 63,000 students, it is one of the biggest universities in Spain. It is one of the oldest universities in both Catalonia and Spain, established in 1450. It is considered one of the best universities in Spain. Overall, the UB has been ranked 1st in Spain in most of the 2022-2023 rankings and is located around the 50th place in Europe. It has 106 departments and more than 5,000 full-time researchers, technicians and research assistants, most of whom work in the 243 research groups as recognized and supported by the Government of Catalonia. In 2010, the UB was awarded 175 national research grants and 17 European grants and participated in over 500 joint research projects with the business sector, generating an overall research income of 70 million euros. The work of these groups is overseen by th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of York
, mottoeng = On the threshold of wisdom , established = , type = Public research university , endowment = £8.0 million , budget = £403.6 million , chancellor = Heather Melville , vice_chancellor = Charlie Jeffery , students = () , undergrad = () , postgrad = () , city = Heslington, York , country = England , campus = Heslington West, Heslington East, and King's Manor , colours = Dark blue and dark green , website = , logo = UoY_logo_with_shield_2016.png , logo_size = 250px , administrative_staff = 3,091 , affiliations = The University of York (abbreviated as or ''York'' for post-nominals) is a collegiate research university, located in the city of York, England. Established in 1963, the university has expanded to more than thirty departments and centres, covering a wide range of subjects. Situated to the south-east of the city of York, the university campus is about in size. The original campus, Campus West, incorporates the York Scien ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vernalis Research
Vernalis Research develops and applies fragment and structure-based methods to drug discovery, and has generated cell active lead compounds and development candidates against biological targets in oncology, neurodegeneration, anti-infectives and inflammation. History Following the sale of Vernalis plc on 10 October 2018, Vernalis Research became a subsidiary of Ligand Holdings UK Ltd, wholly owned by Ligand Pharmaceuticals, Inc. On 2 December 2020, HitGen (Chengdu, China), acquired the entire issued share capital of Vernalis (R&D) Limited. Their scientists, based at Granta Park, Cambridge UK, integrate fragment-based approaches, structural biology, biophysics, assay technology, drug metabolism, pharmacokinetics, cheminformatics, molecular modelling and computational, synthetic organic and medicinal chemistry to enable drug discovery on both established and novel targets, progressing projects from target identification through to clinical candidate. They have generated le ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
