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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] |
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] |
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] |
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] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ser ... [...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] |
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] |
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] |
High-throughput Screening
High-throughput screening (HTS) is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology, materials science and chemistry. Using robotics, data processing/control software, liquid handling devices, and sensitive detectors, high-throughput screening allows a researcher to quickly conduct millions of chemical, genetic, or pharmacological tests. Through this process one can quickly recognize active compounds, antibodies, or genes that modulate a particular biomolecular pathway. The results of these experiments provide starting points for drug design and for understanding the noninteraction or role of a particular location. Assay plate preparation The key labware or testing vessel of HTS is the microtiter plate, which is a small container, usually disposable and made of plastic, that features a grid of small, open divots called ''wells''. In general, microplates for HTS have either 96, 192, 384, 1536, 3456 or 6144 wells. The ... [...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] |
SourceForge
SourceForge is a web service that offers software consumers a centralized online location to control and manage open-source software projects and research business software. It provides source code repository hosting, bug tracking, mirroring of downloads for load balancing, a wiki for documentation, developer and user mailing lists, user-support forums, user-written reviews and ratings, a news bulletin, micro-blog for publishing project updates, and other features. SourceForge was one of the first to offer this service free of charge to open-source projects. Since 2012, the website has run on Apache Allura software. SourceForge offers free hosting and free access to tools for developers of free and open-source software. , the SourceForge repository claimed to host more than 502,000 projects and had more than 3.7 million registered users. Concept SourceForge is a web-based source code repository. It acts as a centralized location for free and open-source software pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fork (software Development)
In software engineering, a project fork happens when developers take a copy of source code from one software package and start independent development on it, creating a distinct and separate piece of software. The term often implies not merely a development branch, but also a split in the developer community; as such, it is a form of schism. Grounds for forking are varying user preferences and stagnated or discontinued development of the original software. Free and open-source software is that which, by definition, may be forked from the original development team without prior permission, and without violating copyright law. However, licensed forks of proprietary software (''e.g.'' Unix) also happen. Etymology The word "fork" has been used to mean "to divide in branches, go separate ways" as early as the 14th century. In the software environment, the word evokes the fork system call, which causes a running process to split itself into two (almost) identical copies that (ty ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitLab
GitLab Inc. is an open-core company that operates GitLab, a DevOps software package which can develop, secure, and operate software. The open source software project was created by Ukrainian developer Dmitriy Zaporozhets and Dutch developer Sytse Sijbrandij. In 2018, GitLab Inc. was considered the first partly-Ukrainian unicorn. Since its foundation, GitLab Inc. promoted remote work, and is known to be among the largest all-remote companies in the world. GitLab has an estimated 30 million registered users, with 1 million being active licensed users. Overview GitLab Inc. was established in 2014 to continue the development of the open-source code-sharing platform launched in 2011 by Dmitriy Zaporozhets. The company's other co-founder Sytse Sijbrandij initially contributed to the project and, by 2012, decided to build a business around it. GitLab offers its platform as a freemium. Since its foundation, GitLab Inc. has been an all-remote company. By 2020, the company employ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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