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Krishna et al. |

RoseTTAFold All-Atom

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Protein Design
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Step 1: Upload your data

Upload a Protein FASTA File

Drag your file(s) or upload
  • Your file can be in the following formats:fasta
    • Important Note!: The file name must be exactly in the format 'filename_.fasta'. For example, 'proteinX_A.fasta'. The .fasta file format, also known as the FASTA format, is a text-based format for representing nucleotide or peptide sequences. Each sequence in a FASTA file is represented by a series of lines, with the first line beginning with a greater-than (>) symbol followed by a description or identifier of the sequence.
or
Don’t have a file?
Use our demo data to run
Use Demo Data

Upload a Nucleic Acid FASTA File(Optional)

Drag your file(s) or upload
  • Your file can be in the following formats:fasta
    • Important Note!: The file name must be exactly in the format 'filename_.fasta'. For example, 'proteinX_A.fasta'. The .fasta file format, also known as the FASTA format, is a text-based format for representing nucleotide or peptide sequences. Each sequence in a FASTA file is represented by a series of lines, with the first line beginning with a greater-than (>) symbol followed by a description or identifier of the sequence.
or
Don’t have a file?
Use our demo data to run
Use Demo Data

Upload a Small Molecule SDF File (Optional)

Drag your file(s) or upload
  • Your file can be in the following formats:sdf
    • The SDF (Structure Data File) format is used to store detailed information about small molecules, including their 3D structures and chemical properties.
or
Don’t have a file?
Use our demo data to run
Use Demo Data
Step 2: Set Parameters
Predicting higher order complexes
DNA

RoseTTAFold All-Atom (RFAA) integrates a residue-based representation for amino acids and DNA bases with an atomic-level representation for all other groups, enabling the modeling of assemblies that include proteins, nucleic acids, small molecules, metals, and covalent modifications based on their sequences and chemical structures.

Example use case: Predicting protein structures

Technology: Neural Networks

Limitation:

  • Predicting covalently modified proteins is not applicable currently. Please contact us if you have any questions.
  • Due to license restrictions, the SignalP 6.0 tool will not be used in job runs.
  • Important: To ensure proper creation of the inference config file in RoseTTAFold All-Atom, we require that FASTA file names follow a specific format. Please rename your FASTA files to match the exact format below:
    • filename_ (e.g., proteinXYZ_A.fasta). The file name must include both the filename and the chain letter, separated by an underscore ('_'). Please see here for more.
  • .fasta
Citation:
Rohith Krishna et al. ,Generalized biomolecular modeling and design with RoseTTAFold All-Atom.Science384,eadl2528(2024).DOI:10.1126/science.adl2528
Released:
Aug-28-2024
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