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With BAR 3.0 and a sequence you can annotate when possible: function (Gene Ontology), structure (Protein Data Bank), protein domains (Pfam). Also if your sequence falls into a cluster with a structural/some structural template/s we provide an alignment towards the template/templates based on the Cluster-HMM (HMM profile) that allows you to ...
PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. Users send a protein sequence and receive a single file with results from database comparisons and prediction methods.
A graph-based algorithm that constructs a graph of the sequence. no [11] SubSeqer: 2008 web: A graph-based approach for the detection and identification of repetitive elements in low–complexity sequences. no [12] ANNIE: 2009 web: This method creates an automation of the sequence analytic process. no [13] LPS-annotate 2011 on request
DeepMind is known to have trained the program on over 170,000 proteins from the Protein Data Bank, a public repository of protein sequences and structures.The program uses a form of attention network, a deep learning technique that focuses on having the AI identify parts of a larger problem, then piece it together to obtain the overall solution. [2]
Amyloidogenicity propensity predictor based on a machine learning approach through recursive feature selection and feed-forward neural networks, taking advantage of newly published sequences with experimental, in vitro, evidence of amyloid formation. sequence - Amyloidogenic regions ArchCandy [37] 2015 Download- BiSMM: Secondary structure-related
Similarly, Light-Attention uses machine learning methods to predict ten different common subcellular locations. [ 12 ] The first model to generalize protein subcellular localization to all cell line does so by leveraging images of subcellular landmark stains (i.e., nuclear, plasma membrane, and endoplasmic reticulum markers) across multiple ...
Casanovo is a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide, enabling de novo peptide sequencing without prior information. [34] InstaNovo Open source
Alignments for membrane protein sequences: Protein: Both: M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest: 2013 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017