A synthetic ribosome binding site (RBS) was generated to drive protein translation at a specified predicted rate using the RBS Calculator online tool (https://www.denovodna.com/)102. All heterologous genes and partial endogenous genes, such as epd (GenBank accession AAC75964.1) and pdxA (Gen...
Protein Design with StructureGPT: a Deep Learning Model for Protein Structure-to-Sequence Translation Nicanor Zalba Sr., Pablo Ursua-Medrano Sr., Humberto Bustince Sr bioRxiv 2024.06.03.597105 • code • Supplementary Adapting protein language models for structure-conditioned design Jeffrey A Ruffolo...
It is intended to provide translation templates, whereby proteins can be efficiently synthesized, as a tool usable in high-throughput post-genomic studies for analyzing structures and functions. A translation template is composed of a coding part optionally together with a PEG part. In case of ...
also see Extended Data Figs.4–6, and see Supplementary Table13for the exact one-sided hypergeometricPvalues and sample sizes. ADRB2, adrenoreceptor beta 2; β-la., β-lactamase; Env, envelope glycoprotein; infA, translation initiation factor 1; MAPK1, mitogen-activated protein kinase 1; Paf...
The silencing mechanisms can either lead to the degradation of a target mRNA, as induced by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), or the suppression of translation of specific mRNAs, as induced by microRNA (miRNA). The focus of this review will be how shRNAs and...
we show that all but one of the knownMinuteloci in the genome correspond to CRP genes - the single exception encodes a subunit of an essential translation initiation factor. Together, these results identify the majority of haploinsufficient loci in theD. melanogastergenome that significantly affect...
Online Mendelian Inheritance in Man – a database of human genes and genetic disorders GO: Gene Ontology that provides a controlled vocabulary to describe gene and gene product attributes UniProt: Universal Protein Resource SwissProt: Protein sequence database InterProScan: It is a tool that scan...
Each miRNA may repress the translation of, and/or destabilize numerous messenger RNAs (mRNAs). Moreover, miRNA genes are frequently organized into genomic clusters [2–4], which are transcribed from a common promoter as polycistronic primary transcripts, and whose coordinate functional roles remain ...
We canonicalize each input residue environment in order to maximize invariance to rotation and translation of the atomic coordinates. For each target residue, we align the N-terminal backbone N − Cα bond to the x axis. We then rotate the structure so that the normal of the N −...
We show examples of how the turnover data may give insights into unknown functions of PTMs and provide a freely accessible online tool that allows interrogation and visualisation of all turnover data. The SPOT methodology is applicable to many cell types and modifications, offering the potential ...