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AutoDock Vina
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 cl ... [...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-based ... [...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] |
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] |
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 Technolog ... [...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, media ... [...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 Architectur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenCL
OpenCL (Open Computing Language) is a framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-programmable gate arrays (FPGAs) and other processors or hardware accelerators. OpenCL specifies programming languages (based on C99, C++14 and C++17) for programming these devices and application programming interfaces (APIs) to control the platform and execute programs on the compute devices. OpenCL provides a standard interface for parallel computing using task- and data-based parallelism. OpenCL is an open standard maintained by the non-profit technology consortium Khronos Group. Conformant implementations are available from Altera, AMD, ARM, Creative, IBM, Imagination, Intel, Nvidia, Qualcomm, Samsung, Vivante, Xilinx, and ZiiLABS. Overview OpenCL views a computing system as consisting of a number of ''compute devices'', which migh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
64-bit Computing
In computer architecture, 64-bit integers, memory addresses, or other data units are those that are 64 bits wide. Also, 64-bit CPUs and ALUs are those that are based on processor registers, address buses, or data buses of that size. A computer that uses such a processor is a 64-bit computer. From the software perspective, 64-bit computing means the use of machine code with 64-bit virtual memory addresses. However, not all 64-bit instruction sets support full 64-bit virtual memory addresses; x86-64 and ARMv8, for example, support only 48 bits of virtual address, with the remaining 16 bits of the virtual address required to be all 0's or all 1's, and several 64-bit instruction sets support fewer than 64 bits of physical memory address. The term ''64-bit'' also describes a generation of computers in which 64-bit processors are the norm. 64 bits is a word size that defines certain classes of computer architecture, buses, memory, and CPUs and, by extension, the software that runs ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Arch Linux
Arch Linux () is an independently developed, x86-64 general-purpose Linux distribution that strives to provide the latest stable versions of most software by following a Rolling release, rolling-release model. The default installation is a minimal base system, configured by the user to only add what is purposely required. #Pacman, Pacman, a package manager written specifically for Arch Linux, is used to install, remove and update Package (package management system), software packages. Arch Linux uses a Rolling release, rolling release model, meaning there are no "major releases" of completely new versions of the system; a regular system update is all that is needed to obtain the latest Arch software; the installation images released every month by the Arch team are simply up-to-date snapshots of the main system components. Arch Linux has comprehensive documentation, consisting of a community-run wiki known as the ArchWiki. History Inspired by CRUX, another minimalist distrib ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fedora (operating System)
Fedora Linux is a Linux distribution developed by the Fedora Project. Fedora contains software distributed under various free and open-source licenses and aims to be on the leading edge of open-source technologies. Fedora is the upstream (software development), upstream source for Red Hat Enterprise Linux. Since the release of Fedora 35, six different editions are made available tailored to personal computer, server (computing), server, cloud computing, Container (computing), container and Internet of Things installations. A new version of Fedora Linux is released every six months. , Fedora Linux has an estimated 1.2 million users, including Linus Torvalds (), creator of the Linux kernel. Features Fedora has a reputation for focusing on innovation, integrating new technologies early on and working closely with Upstream (software development), upstream Linux communities. Making changes upstream instead of specifically for Fedora Linux ensures that the changes are available t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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