QuoteTarget: A sequence‐based transformer protein language model to identify potentially druggable protein targets
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4555
Abstract: The development of efficient computational methods for drug target protein identification can compensate for the high cost of experiments and is therefore of great significance for drug development. However, existing structure‐based drug target protein‐identification algorithms… read more here.
Keywords: sequence based; drug target; drug; protein ... See more keywords
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach
Sign Up to like & getrecommendations! Published in 2017 at "Plant Cell Reports"
DOI: 10.1007/s00299-017-2157-5
Abstract: Key messageExcluding polymorphic probes from GeneChip®transcript profiling experiments via a sequence-based approach results in improved detection of differentially expressed genes in developing seeds ofArabidopsis thalianaaccessions Col-0 and C24.AbstractGeneChip® arrays represent a powerful tool for transcript… read more here.
Keywords: arabidopsis thaliana; transcript profiling; thaliana accessions; sequence based ... See more keywords
The unbearable lightness of sequenced-based identification
Sign Up to like & getrecommendations! Published in 2019 at "Fungal Diversity"
DOI: 10.1007/s13225-019-00428-3
Abstract: Using the basic GenBank local alignment search tool program (BLAST) to identify fungi collected in a recently protected beech forest at Montricher (Switzerland), the number of ITS sequences associated to the wrong taxon name appears… read more here.
Keywords: unbearable lightness; lightness sequenced; sequence based; identification ... See more keywords
Machine learning techniques for sequence-based prediction of viral–host interactions between SARS-CoV-2 and human proteins
Sign Up to like & getrecommendations! Published in 2020 at "Biomedical Journal"
DOI: 10.1016/j.bj.2020.08.003
Abstract: Background COVID-19 (Coronavirus Disease-19), a disease caused by the SARS-CoV-2 virus, has been declared as a pandemic by the World Health Organization on March 11, 2020. Over 15 million people have already been affected worldwide… read more here.
Keywords: sars cov; human proteins; machine learning; sequence based ... See more keywords
A new sequence based encoding for prediction of host-pathogen protein interactions
Sign Up to like & getrecommendations! Published in 2019 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2018.12.001
Abstract: Pathogen-host interactions are very important to figure out the infection process at the molecular level, where pathogen proteins physically bind to human proteins to manipulate critical biological processes in the host cell. Data scarcity and… read more here.
Keywords: pathogen; pathogen host; sequence based; host ... See more keywords
Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka.
Sign Up to like & getrecommendations! Published in 2018 at "Human immunology"
DOI: 10.1016/j.humimm.2017.12.007
Abstract: DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 714 healthy adult blood bank donors from Colombo, Sri Lanka, to characterize allele frequencies in support of studies… read more here.
Keywords: colombo sri; sequence based; hla; sri lanka ... See more keywords
Sequence-based determinants and prediction of fuzzy interactions in protein complexes.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of molecular biology"
DOI: 10.1016/j.jmb.2020.02.017
Abstract: It is becoming increasingly recognized that intrinsically disordered proteins are involved in a wide variety of protein interaction modes. In addition to the well-known process of 'folding upon binding' (disorder-to-order transition), many examples of fuzzy… read more here.
Keywords: fuzzy interactions; disorder; sequence based; based determinants ... See more keywords
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Cell"
DOI: 10.1016/j.molcel.2018.03.035
Abstract: (Molecular Cell 63, 337–346; July 21, 2016) As a result of an author oversight in the originally published version of this article, the Rosetta script file design.xml provided in Data S1 was missing the res_type_constraint… read more here.
Keywords: structure sequence; sequence based; automated structure; xml ... See more keywords
Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates
Sign Up to like & getrecommendations! Published in 2022 at "Biochemistry"
DOI: 10.1021/acs.biochem.2c00499
Abstract: Various neurological dysfunctions are associated with cytotoxic amyloid-containing aggregates formed through the irreversible maturation of protein condensates generated by phase separation. Here, we investigate the amino acid code for this cytotoxicity using TDP-43 deep-sequencing data.… read more here.
Keywords: based prediction; aggregation; sequence based; cytotoxicity ... See more keywords
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00799
Abstract: An essential step in engineering proteins and understanding disease-causing missense mutations is to accurately model protein stability changes when such mutations occur. Here, we developed a new sequence-based predictor for the protein stability (PROST) change… read more here.
Keywords: protein stability; prost; sequence based; predictor ... See more keywords
A sequence-based computational method for prediction of MoRFs
Sign Up to like & getrecommendations! Published in 2017 at "RSC Advances"
DOI: 10.1039/c6ra27161h
Abstract: Molecular recognition features (MoRFs) are relatively short segments (10–70 residues) within intrinsically disordered regions (IDRs) that can undergo disorder-to-order transitions during binding to partner proteins. Since MoRFs play key roles in important biological processes such… read more here.
Keywords: morfs; sequence based; computational method; based computational ... See more keywords