FPbaseにmStayGoldとmBaoJin a.k.a. mStayGoldが別々に掲載されてるけどそんなことある……？別のものにmStayGoldって名付けられてる……？

RFPさんはちゃんと名前（DsRed）で呼んでもらってるのに、GFPさんは名前で呼んでもらってない！ FPのみんなは不安よな。FPbase、動きます。

OptoBase: a web platform for molecular optogenetics Platform on Molecular Optogenetics pubs.acs.org/doi/10.1021/acs… OptoBase OptoBase is an online platform for molecular optogenetics. At its core is a hand-annotated and ontology-supported database that aims to cover all existing optogenetic switches and publications, which is further complemented with a collection of convenient optogenetics-related web tools. optobase.org/ OPTICS: An interactive online platform for photosensory and bio-functional proteins in optogenetic systems Over the past decade, hundreds of optogenetic systems (OSs) have been developed for various applications from living cells to freely moving organisms. However, no database has been constructed to comprehensively provide the valuable information of optogenetic systems (OSs) yet. In this work, a new database named OPTICS (an interactive online platform for photosensory and bio-functional proteins in optogenetic systems) is introduced. OPTICS is unique in (i) systematically describing diverse optogenetic systems (OSs) from the perspective of photoreceptor-based classification and mechanism of action; (ii) featuring the detailed biophysical properties and functional data of OSs; (iii) providing the interaction between optogenetic tools (OT) and cellular bio-functional proteins (CP) for each optogenetic system (OS) referring to distinct applications in research, diagnosis, and therapy, and (iv) enabling a light response property-based search against all OSs in the database. Since the information on OSs is essential for rapid and predictable design of optogenetic controls, the comprehensive data provided in OPTICS lay a solid foundation for the future development of novel OSs. zenodo.org/records/8369851 optics.idrblab.net/ optics.idrblab.net/about Fluorescent Biosensor Database (FBDB) The Genetically Encodable Fluorescent Protein Biosensor Database is a repository of the array of fluorescent biosensors developed to study cell signaling in live cells. biosensordb.ucsd.edu/ A fluorescent protein database (FPbase) FPbase is a free and open-source, community-editable database for fluorescent proteins (FPs) and their properties. Each protein in the database has a dedicated page showing amino acid sequence, accession IDs (e.g. GenBank, UniProt), evolution lineages and mutations, fluorescence attributes, structural data, references that introduced or characterized the protein, and more. fpbase.org/ FPbase Database Schema The database schema determines the fields and information that can be stored for any given object in the database, and how the objects relate to each other. The schema changes periodically to accommodate new fields, or to add features to the site. help.fpbase.org/schema/schem… 📃 Protein design accelerates the development and application of optogenetic tools (OT) This article emphasizes the pivotal role of protein design in the development of optogenetic tools, offering insights into potential future directions. We begin by providing an introduction to the historical development and fundamental principles of optogenetics, followed by an exploration of the operational mechanisms of key photosensitive domains, which includes clarifying the conformational changes they undergo in response to light, such as allosteric modulation and dimerization processes. Building on this foundation, we reveal the development of protein design tools that will enable the creation of even more sophisticated optogenetic techniques. pmc.ncbi.nlm.nih.gov/article… 📃 An optogenetic gene expression system with rapid activation and deactivation kinetics Our approach utilizes an engineered version of EL222, a bacterial Light-Oxygen-Voltage (LOV) protein that binds DNA when illuminated with blue light. With this system, we achieve light-gated transcription in several mammalian cell lines and intact zebrafish embryos with minimal basal gene activation and toxicity. pmc.ncbi.nlm.nih.gov/article…

FPbaseで3~4分はいけそうだな

reminder that FPbase exists

I just posted another guest lecture from our recent Microtutor LIVE course. This one is on the Fluorescent Protein Database, FPbase, by creator @TalleyJLambert. Enjoy! youtu.be/nETkUNQ48Sg?si=O8KZ…

Good sleuth work haha. I noticed the differences in lineage on FPBase too! We’ll probably just test a couple 🤷

@fpbase creator @TalleyJLambert will show our students how to build a custom fluorescence spectraviewer for their microscopes #microtutorLIVE

The two mCherry variants above are smaller than 96% of fluorescent proteins in FPbase. AFAICT, any FPbase entry shorter than these seems to require some cofactor like flavin or bilirubin for fluorescence. 5/

I checked FPbase for the GFP with the longest maturation time. It's mmGFP fpbase.org/protein/mmgfp/ with a maturation time of 1440 min, which also has that Q94W mutation (and many others).

Using this hype-filled drivel to claim anything about whether design is/was a bottleneck is kinda silly. It’s a look-up table that interpolated across FPbase to design “new” GFPs with a lot of fancy buzzwords to confuse the non-experts.

mScarlet3 all the way !

mJerry? 🍒

Mturquoise for you 😊 as well as msfGFP2 and mstaygold. miRFP670nano3 for the size but if mstgold could be turn in red or far red would be amazing.

The @FPbase has data on >1000 fluorescent proteins What's your favorite?

Quick! Who's going to sumit the #1000? @fpbase

I love this website

When you don't exactly know which FP you have, just use FP blast, another fine feature of @FPbase

You can never have enough FPs, as long as you deposit the fluorescent specra on FPbase

Love it! Would be a cool addition to @FPbase An option to upload your own data would make it a super useful tool to analyse bleaching data in a standardized way !!