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AutoDock
AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the research community. It is used by the FightAIDS@Home and OpenPandemics - COVID-19 projects run at World Community Grid, to search for antivirals against HIV/AIDS and COVID-19. In February 2007, a search of the ISI Citation Index showed more than 1,100 publications had been cited using the primary AutoDock method papers. As of 2009, this number surpassed 1,200. AutoDock Vina is a successor of AutoDock, significantly improved in terms of accuracy and performance. It is available under the Apache license. Both AutoDock and Vina are currently maintained by Scripps Research, specifically the Center for Computational Structural Biology (CCSB) led by Dr. Arthur J. Olson AutoDock is widely used and played a role in the development of the first c ... [...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 nov ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
World Community Grid
World Community Grid (WCG) is an effort to create the world's largest volunteer computing platform to tackle scientific research that benefits humanity. Launched on November 16, 2004, with proprietary Grid MP client from United Devices and adding support for Berkeley Open Infrastructure for Network Computing (BOINC) in 2005, World Community Grid eventually discontinued the Grid MP client and consolidated on the BOINC platform in 2008. In September 2021, it was announced that IBM transferred ownership to the Krembil Research Institute of University Health Network in Toronto, Ontario. World Community Grid utilizes unused processing power of consumer devices (PCs, Laptops, Android Smartphones, etc.) to analyse data created by the research groups that participate in the grid. WCG projects have analysed data related to the human genome, the human microbiome, HIV, dengue, muscular dystrophy, cancer, influenza, Ebola, Zika virus, virtual screening, rice crop yields, clean energy, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FightAIDS@Home
FightAIDS@Home ("Fight AIDS at home") is a volunteer computing project operated by the Olson Laboratory at The Scripps Research Institute. It runs on internet-connected home computers, and since July 2013 also runs on Android smartphones and tablets. It aims to use biomedical software simulation techniques to search for ways to cure or prevent the spread of HIV/AIDS. Methods Olson's target is HIV protease, a key molecular machine of the virus that when blocked stops it from maturing. These blockers, known as "protease inhibitors", are thus a way of avoiding the onset of AIDS and prolonging life. The Olson Laboratory is using computational methods to identify new candidate drugs that have the right shape and chemical characteristics to block HIV protease. This general approach is called structure-based drug design, and according to the National Institutes of Health's National Institute of General Medical Sciences, it has already had a dramatic effect on the lives of people living ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
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 b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scripps Research
Scripps Research, previously known as The Scripps Research Institute (TSRI), is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institute has over 170 laboratories employing 2,100 scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. The institute holds over 1,100 patents, has produced 11 FDA-approved therapeutics, and has generated over 50 spin-off companies. According to the 2017 Nature Innovation Index, Scripps Research is the #1 most influential research institution in the world. The Scripps Research graduate program is ranked 9th nationally in the biological sciences, 6th for organic chemistry, and 6th for biochemistry. In 2022, their Jupiter, FL campus became a part of the University of Florida. Jupiter-base ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Debian
Debian (), also known as Debian GNU/Linux, is a Linux distribution composed of free and open-source software, developed by the community-supported Debian Project, which was established by Ian Murdock on August 16, 1993. The first version of Debian (0.01) was released on September 15, 1993, and its first stable version (1.1) was released on June 17, 1996. The Debian Stable branch is the most popular edition for personal computers and servers. Debian is also the basis for many other distributions, most notably Ubuntu. Debian is one of the oldest operating systems based on the Linux kernel. The project is coordinated over the Internet by a team of volunteers guided by the Debian Project Leader and three foundational documents: the Debian Social Contract, the Debian Constitution, and the Debian Free Software Guidelines. New distributions are updated continually, and the next candidate is released after a time-based freeze. Since its founding, Debian has been developed openly a ... [...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 disco ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. History VMD has been developed under the aegis of principal investigator Klaus Schulten in the Theoretical and Computational Biophysics group at the Beckman Institute for Advanced Science and Technolo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nvidia
Nvidia CorporationOfficially written as NVIDIA and stylized in its logo as VIDIA with the lowercase "n" the same height as the uppercase "VIDIA"; formerly stylized as VIDIA with a large italicized lowercase "n" on products from the mid 1990s to early-mid 2000s. Though unofficial, second letter capitalization of NVIDIA, i.e. nVidia, may be found within enthusiast communities and publications. ( ) is an American multinational technology company incorporated in Delaware and based in Santa Clara, California. It is a software and fabless company which designs graphics processing units (GPUs), application programming interface (APIs) for data science and high-performance computing as well as system on a chip units (SoCs) for the mobile computing and automotive market. Nvidia is a global leader in artificial intelligence hardware and software. Its professional line of GPUs are used in workstations for applications in such fields as architecture, engineering and construction, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CUDA
CUDA (or Compute Unified Device Architecture) is a parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for general purpose processing, an approach called general-purpose computing on GPUs ( GPGPU). CUDA is a software layer that gives direct access to the GPU's virtual instruction set and parallel computational elements, for the execution of compute kernels. CUDA is designed to work with programming languages such as C, C++, and Fortran. This accessibility makes it easier for specialists in parallel programming to use GPU resources, in contrast to prior APIs like Direct3D and OpenGL, which required advanced skills in graphics programming. CUDA-powered GPUs also support programming frameworks such as OpenMP, OpenACC and OpenCL; and HIP by compiling such code to CUDA. CUDA was created by Nvidia. When it was first introduced, the name was an acronym for Compute Unified Device ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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