Book Chapter10.1016/B978-0-12-809633-8.20267-7
Secondary Structure Prediction
Jonas Reeb,Burkhard Rost +1 more
- 01 Jan 2019
- pp 488-496
25
TL;DR: In protein secondary structure prediction, secondary structure predictions can help in expert annotations and are used as input for many automated annotation tools as discussed by the authors, which is the most fundamental second step in finding out anything about those sequences.
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Abstract: Information about the structure and function of a protein are encoded in its amino acid sequence. Continued progress in sequencing increasingly explodes the number of proteins for which the sequences are known but little other knowledge exists. After database searches through alignments, protein secondary structure predictions might be the most fundamental second step in finding out anything about those sequences. Secondary structure predictions can help in expert annotations and are used as input for many automated annotation tools. Today’s top prediction methods reach high levels of performance at relatively little computational costs.
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References
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
BLAST+: architecture and applications.
Christiam Camacho,George Coulouris,Vahram Avagyan,Ning Ma,Jason S. Papadopoulos,Kevin Bealer,Thomas L. Madden +6 more
TL;DR: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences.
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
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