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nav:
  - index.md
  - Tutorials:
      - tutorials/index.md
      - Install Folding Studio: tutorials/installation.md
      - Run AlphaFold2 on a protein sequence: tutorials/single_folding_job_af2.md
      - Perform a Multiple Sequence Alignment (MSA) search: tutorials/msa_search.md
      - Preview - Run folding jobs with AlphaFold3-like models: tutorials/single_folding_job_af3.md
  - How-to guides:
      - how-to-guides/index.md
      - AlphaFold2/OpenFold:
          - Provide Input Data: how-to-guides/af2_openfold/provide_input_data.md
          - Launch a Folding Job using AlphaFold2: how-to-guides/af2_openfold/single_af2_job.md
          - Launch a Folding Job using OpenFold: how-to-guides/af2_openfold/single_openfold_job.md
          - Launch a Folding Job with custom parameters: how-to-guides/af2_openfold/set_af_folding_parameters.md
          - Launch a batch Folding Job from a configuration file: how-to-guides/af2_openfold/batch_job_from_configuration_file.md
          - Launch a batch Folding Job from a directory of fasta files: how-to-guides/af2_openfold/batch_job_from_directory.md
          - Check Job Status: how-to-guides/af2_openfold/fetch_folding_job_status.md
          - Download Job Logs: how-to-guides/af2_openfold/download_logs.md
          - Cancel a Folding Job submission: how-to-guides/af2_openfold/cancel_experiment.md
          - Retrieve Features from a Folding Job: how-to-guides/af2_openfold/get_experiment_features.md
          - Download results of a folding job: how-to-guides/af2_openfold/download_prediction_results.md
          - Advanced Algorithms:
              - Launch a Folding Job using MSA subsampling: how-to-guides/af2_openfold/advanced_algorithms/msa_subsampling_job.md
              - Launch a Folding Job using the Gap Trick for Folding Multimer Complexes: how-to-guides/af2_openfold/advanced_algorithms/gap_trick_job.md
              - Launch a Folding Job using an Initial Guess Structure in AlphaFold2: how-to-guides/af2_openfold/advanced_algorithms/initial_guess_af2.md
              - Launch a Folding Job applying Template Masking in Gap Trick Mode: how-to-guides/af2_openfold/advanced_algorithms/template_masking_job.md
          - Preview - Launch a folding job using SoloSeq model: how-to-guides/af2_openfold/soloseq_job.md
      - Preview - AlphaFold3-like:
          - Provide Input Data: how-to-guides/af3/provide_input_data.md
          - Launch a Single Job using Boltz-1: how-to-guides/af3/single_job_boltz.md
          - Launch a Single Job using Chai-1: how-to-guides/af3/single_job_chai.md
          - Launch a Single Job using Protenix: how-to-guides/af3/single_job_protenix.md
          - Launch a Single Job from a YAML file using Boltz-1: how-to-guides/af3/boltz_single_yaml_job.md
          - Launch a Batch Job from a directory: how-to-guides/af3/batch_job_from_directory.md
          - Launch a Single Job from a Protein Sequence: how-to-guides/af3/single_job_from_protein_sequence.md
      - Post-processing recipes:
          - Calculate Interface pLDDT and pAE: how-to-guides/other/pLDDT_pAE_calculation.md
      - Multiple Sequence Alignment Search:
          - Provide Input Data for MSA: how-to-guides/msa_search/provide_input_data.md
          - Launch an MSA Search with MMSeqs2: how-to-guides/msa_search/msa_search_mmseqs2.md
          - Launch an MSA Search ignoring cache: how-to-guides/msa_search/msa_no_cache.md
          - Check an MSA Job Status: how-to-guides/msa_search/fetch_msa_job_status.md
          - Download MSA Job Logs: how-to-guides/msa_search/download_msa_logs.md
          - Download Results of an MSA Search: how-to-guides/msa_search/download_msa_search_results.md
  - Explanation:
      - explanation/index.md
      - Supported models: explanation/supported_models.md
      - Advanced algorithms: explanation/advanced_algorithms.md
  - Reference:
      - CLI: reference/cli.md
      - Python Library: reference/python_lib_docs.md
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site_name: Folding Studio
site_url: https://int-bio-foldingstudio-gcp.nw.r.appspot.com
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