ColabFold: making protein folding accessible to all
TL;DR: ColabFold as discussed by the authors combines the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold for protein folding and achieves 40-60fold faster search and optimized model utilization.
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Abstract: ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40-60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at https://github.com/sokrypton/ColabFold and its novel environmental databases are available at https://colabfold.mmseqs.com .
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References
Matplotlib: A 2D Graphics Environment
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
34.7K
Highly accurate protein structure prediction with AlphaFold
John M. Jumper,Richard O. Evans,Alexander Pritzel,Tim Green,Michael Figurnov,Olaf Ronneberger,Kathryn Tunyasuvunakool,Russell Bates,Augustin Žídek,Anna Potapenko,Alex Bridgland,Clemens Meyer,Simon A. A. Kohl,Andrew J. Ballard,Andrew Cowie,Bernardino Romera-Paredes,Stanislav Nikolov,R. D. Jain,Jonas Adler,Trevor Back,Stig Petersen,David Reiman,Ellen Clancy,Michal Zielinski,Martin Steinegger,Michalina Pacholska,Tamas Berghammer,Sebastian Bodenstein,David L. Silver,Oriol Vinyals,Andrew W. Senior,Koray Kavukcuoglu,Pushmeet Kohli,Demis Hassabis +33 more
TL;DR: For example, AlphaFold as mentioned in this paper predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture. But the accuracy is limited by the fact that no homologous structure is available.
•Book
Accelerated Profile HMM Searches
Sean R. Eddy
- 01 May 2015
TL;DR: An acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm, which computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment.
Pfam: The protein families database in 2021.
Jaina Mistry,Sara Chuguransky,Lowri Williams,Matloob Qureshi,Gustavo A. Salazar,Erik L. L. Sonnhammer,Silvio C. E. Tosatto,Lisanna Paladin,Shriya Raj,Lorna Richardson,Robert D. Finn,Alex Bateman +11 more
TL;DR: The Pfam database is a widely used resource for classifying protein sequences into families and domains and the reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family.
5.6K