<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36755?offset=360 https://bioinformaticsonline.com/bookmarks/view/37937/frodock-20-fast-protein%E2%80%93protein-docking-server Wed, 17 Oct 2018 04:31:30 -0500 https://bioinformaticsonline.com/bookmarks/view/37937/frodock-20-fast-protein%E2%80%93protein-docking-server <![CDATA[FRODOCK 2.0: fast protein–protein docking server]]> frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein–protein binding conformations that can be further refined with more computationally demanding strategies.

Address of the bookmark: http://frodock.chaconlab.org/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/40389/sequila-cov-a-fast-and-scalable-library-for-depth-of-coverage-calculations Sun, 15 Dec 2019 10:19:35 -0600 https://bioinformaticsonline.com/bookmarks/view/40389/sequila-cov-a-fast-and-scalable-library-for-depth-of-coverage-calculations <![CDATA[SeQuiLa-cov: A fast and scalable library for depth of coverage calculations]]> The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation site http://biodatageeks.org/sequila/benchmarking/benchmarking.html#depth-of-coverage. An archival copy of the code and supporting data is also available via the GigaScience database GigaDB

• Project name: SeQuiLa-cov

• Project home page: http://biodatageeks.org/sequila/

• Source code repository: https://github.com/ZSI-Bio/bdg-sequila

• Operating system: Platform independent

• Programming language: Scala

• Other requirements: Docker

• License: Apache License 2.0

Address of the bookmark: https://academic.oup.com/gigascience/article/8/8/giz094/5543653

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Mon, 18 Jan 2021 10:47:56 -0600 https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite <![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]> MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

]]> Manisha Mishra