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Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments [PDF]

BMC Bioinformatics, 2021
Background The use of sound to represent sequence data—sonification—has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance more effectively.
Edward J. Martin, Thomas R. Meagher, Daniel Barker   +2 more
doaj   +6 more sources

Protein sequence databases [PDF]

Current Opinion in Chemical Biology, 2000
A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each ...
Apweiler, Rolf, Bairoch, Amos Marc, Wu, Cathy H   +2 more
openaire   +5 more sources

The constraints between amino acids influence the unequal distribution of codons and protein sequence evolution

Royal Society Open Science, 2021
Four nucleotides (A, U, C and G) constitute 64 codons at free combination but 64 codons are unequally assigned to 21 items (20 amino acids plus one stop). About 500 amino acids are known but only 20 are selected to make up the proteins.
Yi Qian, Rui Zhang, Xinglu Jiang, Guoqiu Wu   +3 more
doaj   +1 more source

Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond

Biomolecules, 2022
AlphaFold2 (AF2) has created a breakthrough in biology by providing three-dimensional structure models for whole-proteome sequences, with unprecedented levels of accuracy.
Apolline Bruley, Jean-Paul Mornon, Elodie Duprat, Isabelle Callebaut   +3 more
doaj   +1 more source

ML-DTD: Machine Learning-Based Drug Target Discovery for the Potential Treatment of COVID-19

Vaccines, 2022
Recent research has highlighted that a large section of druggable protein targets in the Human interactome remains unexplored for various diseases. It might lead to the drug repurposing study and help in the in-silico prediction of new drug-human protein
Sovan Saha, Piyali Chatterjee, Anup Kumar Halder, Mita Nasipuri, Subhadip Basu, Dariusz Plewczynski   +5 more
doaj   +1 more source

Protein Sequence Retrieval and Phylogenetic Analysis of Various α-amylase Producing Bacillus species [PDF]

International Journal Bioautomation, 2020
Due to advancements made in biotechnology, genetic manipulation and medium optimization has been possible and that has led to high yield in enzyme especially α-amylase with improvised properties that find its application suitably in detergent, laundry ...
Sonali Priyadarshini, Sukanta Kumar Pradhan, Pratima Ray   +2 more
doaj   +1 more source

Complete Sequences of the Velvet Worm Slime Proteins Reveal that Slime Formation is Enabled by Disulfide Bonds and Intrinsically Disordered Regions

Advanced Science, 2022
The slime of velvet worms (Onychophora) is a strong and fully biodegradable protein material, which upon ejection undergoes a fast liquid‐to‐solid transition to ensnare prey.
Yang Lu, Bhargy Sharma, Wei Long Soon, Xiangyan Shi, Tianyun Zhao, Yan Ting Lim, Radoslaw M. Sobota, Shawn Hoon, Giovanni Pilloni, Adam Usadi, Konstantin Pervushin, Ali Miserez   +11 more
doaj   +1 more source

Quantitative Analysis of Protein Evolution: The Phylogeny of Osteopontin

Frontiers in Genetics, 2021
The phylogenetic analysis of proteins conventionally relies on the evaluation of amino acid sequences or coding sequences. Individual amino acids have measurable features that allow the translation from strings of letters (amino acids or bases) into ...
Xia Wang, Georg F. Weber
doaj   +1 more source

Protein Ladder Sequencing [PDF]

Science, 1993
A new approach to protein sequencing is described. It consists of two steps: (i) ladder-generating chemistry, the controlled generation from a polypeptide chain by wet chemistry of a family of sequence-defining peptide fragments, each differing from the next by one amino acid; and (ii) data readout, a one-step readout of the resulting protein ...
B T, Chait, R, Wang, R C, Beavis, S B, Kent   +3 more
openaire   +2 more sources

PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms

Frontiers in Genetics, 2022
Protein function prediction is gradually emerging as an essential field in biological and computational studies. Though the latter has clinched a significant footprint, it has been observed that the application of computational information gathered from ...
Kaustav Sengupta, Kaustav Sengupta, Kaustav Sengupta, Sovan Saha, Anup Kumar Halder, Anup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Subhadip Basu, Dariusz Plewczynski, Dariusz Plewczynski   +10 more
doaj   +1 more source