Conformational Space of Short Peptides

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/short_peptides-dataset")

fs.listdir("s3://toyokounqpeptides/tripep/")

Description:

Co-managed by Toyoko and the Structural Biology Group at the Universidad Nacional de Quilmes, this dataset allows us to explore the conformational space of all possible peptides using the 20 common amino acids. It consists of a collection of exhaustive molecular dynamics simulations of tripeptides and pentapeptides.

Contact:

Co-managed by Toyoko and the Structural Biology Group at the Universidad Nacional de Quilmes, this dataset allows us to explore the conformational space of all possible peptides using the 20 common amino acids. It consists of a collection of exhaustive molecular dynamics simulations of tripeptides and pentapeptides.

Update Frequency:

Not updated

Managed By:

https://www.toyoko.io/

Resources:

1. resource:

   • Description: Tri-peptides. All possible 8000 tri-peptides, 2 replicas. File types: Amber .out, .traj and .crd. To retrieve files use this format: N{AA}{AA}C{AA}-R{replic_number}.dmd.1.{ext}, for example, for ALA-SER-ASN traj file for replica 2, the name is NALASERCASN-R2.dmd.1.traj
   • ARN: arn:aws:s3:::toyokounqpeptides/tripep/
   • Region: us-west-2
   • Type: S3 Bucket

2. resource:

   • Description: Penta-peptides. All possible 3200000 penta-peptides, no replicas. File types: .tar.bz2. To retrieve files use this format: N{AA}{AA}{AA}{AA}C{AA}-R1.tar.bz2
   • ARN: arn:aws:s3:::toyokounqpeptides/5pep/
   • Region: us-west-2
   • Type: S3 Bucket

Tags:

aws-pds, amino acid, bioinformatics, biomolecular modeling, molecular dynamics, protein, structural biology, life sciences

Tutorials:

1. tutorial:
   • Title: Intro to Conformational Space of Short Peptides
   • URL: https://www.toyoko.io/pepdataset/
   • AuthorName: Sebastian Bassi and Virginia Gonzalez
   • AuthorURL: https://about.me/bassi