tinchogb/RNA_stuff

Information about typical RNA sites, meetings, tools, databases, etc.

RNA_stuff

In this README you can find diverse information about typical RNA sites, meetings, tools, databases, etc.

I also leave you copy (in spanish) of my degree final work that was about Conformational diversity in RNAs.

Please, feel free to improve and add information.

RNA typical web-sites

• The RNA society site, and their twitter
• Sweden RNA site (look the researchers section if there is anyone known)
• The RNA institute
• The G4 Society

RNA anual meetings:

• 2020 CANADA, from RNA society
• 2019 SWEDEN, rna society in sweden (made in Sep-2019, maybe in 2020 could be the next one)
• Rustbelt
• 2020 USA, The RNA institute meeting
• 2020 SWEDEN, IRT NNN

RNA structural competition

• RNA Puzzles, a CASP-like.
  • Recent paper (2019-12-04)

Common databases:

• Sequences
  • Rfam, (RNA families)
  • RNACentral, (non-coding RNAs from 40 curated databases)
• Structures
  • PDB and NDB
  • RNArchitecture
  • SCOR (down)
  • URS
  • BGSU RNA site
  • Cosmos database
  • Metal PDB
  • RNA topology using graph theory
  • RNA virus (new v3)
  • 5S rRNA Database
• Residues
  • The RNA modification database
  • RNA basepair database
  • RNABP COGEST (has another links basepair databases inside)
• Others
  • NCRNA Databases
  • 3D RNA rotamers (Richardsons Lab)
  • Chemical mapping data

Groups:

• Bujnicki (one of the best, has softwares, databases, etc)
• Znosko

Tools:

• X3DNA (Xiang-Jun Lu, DSSR forum, web 3XDNA)
• rna-tools (Magnus from Bujnicki group)
• R3D-BLAST2 (search substructures using structural alphabet)
• RNAflex (using SVM)
• RBP Motif Search

Papers:

• RNA 3D prediction
  • Homology
    • RNA 3D structure prediction guided by independent folding of homologous sequences.
• RNA 3D contacts
  • ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.