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- Protein ALignment And Detection INterface PALADIN is a protein sequence alignment tool designed for the accurate functional characterizati3 KB (361 words) - 18:31, 10 June 2022
- AlphaPulldown, a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers Yu,D. et al. (2022) AlphaPulldown – a Python package for protein-protein interaction screens using AlphaFold-Multimer. Bioinformatics, Volume 39, Is3 KB (300 words) - 14:11, 10 July 2023
- .../or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux sys3 KB (364 words) - 19:53, 12 August 2022
- ...es that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s.3 KB (344 words) - 19:55, 12 August 2022
- PLAST is a parallel alignment search tool for comparing large protein banks. * Protein vs protein (plastp), protein vs nucleotide (tplastn),3 KB (320 words) - 20:23, 12 August 2022
- * SSpro release 6.0 (2021) : Protein secondary structure prediction (3-class) * SSpro8 release 6.0 (2021) : Protein secondary structure prediction (8-class)3 KB (381 words) - 20:35, 12 August 2022
- ...n prediction, which is based on the PSORT principle. WoLF PSORT converts a protein's amino acid sequences into numerical localization features; based on sorti "Protein Subcellular Localization Prediction with WoLF PSORT",3 KB (309 words) - 21:29, 6 December 2019
- ...aligners to compute BLASTX-like alignments between sequencing reads and a protein database in a small fraction of the time required by BLASTX. The PAUDA appr ...l H. Huson and Chao Xie, A poor man’s BLASTX - high-throughput metagenomic protein database search using PAUDA, submitted to HitSeq (2013).]3 KB (367 words) - 17:03, 21 August 2022
- ...here the path leads through solvent occupied space without penetrating the protein surface.3 KB (345 words) - 16:47, 28 February 2023
- ...PSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100 times speedup as compared to BLASTX (for reads of3 KB (304 words) - 21:24, 6 December 2019
- reCOGnizer is a user-friendly implementation of protein functional identification using COG database. ...ead, significantly increasing the speed of the most time intensive step of protein annotation.3 KB (327 words) - 17:03, 3 December 2020
- ...substitution is defined as recurrent substitutions that occur at the same protein site in multiple independent branches. If multiple substitutions result in * Error-corrected rate of protein convergence with null expectation obtained by:3 KB (380 words) - 22:12, 26 July 2023
- ...3th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13) competition in the data-assisted targets cate JL MacCallum, A Perez, and KA Dill, Determining protein structures by combining semireliable data with atomistic physical models by3 KB (318 words) - 18:35, 18 August 2022
- ...iple alignment of family-specific sequences. Therefore, in addition to the protein domain classfication according to the Pfam database, UProC can, in principl Meinicke, Peter. '''UProC: tools for ultra-fast protein domain classification'''. ''Bioinformatics'', 20143 KB (418 words) - 20:53, 12 August 2022
- ...diction of peptide-protein interactions, including not only binary peptide-protein interactions, but also corresponding peptide binding residues.2 KB (255 words) - 18:00, 23 May 2022
- ...o acid substitution or indel has an impact on the biological function of a protein. ...substitutions and a single AA deletion at every amino acid position of all protein sequences in human and mouse.3 KB (350 words) - 20:27, 12 August 2022
- ...CI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is e ...eng Chen and Yi Zhao* Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research (2013), doi:3 KB (374 words) - 14:09, 23 April 2021
- ...arkers in metagenomic data and determine the presence and abundance of the protein families of interest.2 KB (287 words) - 16:12, 24 November 2020
- PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iC ...1364-2 Krakau S, Richard H, Marsico A: PureCLIP: Capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. Genome Bio2 KB (285 words) - 21:24, 6 December 2019
- ...and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API2 KB (294 words) - 19:38, 21 August 2022