# AlphaFold 3

## Docs

- [Batch Processing Multiple Inputs](https://mintlify.wiki/google-deepmind/alphafold3/advanced/batch-processing.md): Learn how to efficiently process multiple AlphaFold 3 predictions using batch processing and optimization techniques
- [Specifying Covalent Bonds](https://mintlify.wiki/google-deepmind/alphafold3/advanced/covalent-bonds.md): Learn how to specify covalent bonds between entities in AlphaFold 3 for modeling covalent ligands and glycans
- [Providing Custom MSA Data](https://mintlify.wiki/google-deepmind/alphafold3/advanced/custom-msa.md): Learn how to provide custom Multiple Sequence Alignments for protein and RNA chains in AlphaFold 3
- [Providing Custom Structural Templates](https://mintlify.wiki/google-deepmind/alphafold3/advanced/custom-templates.md): Learn how to provide custom structural templates for protein chains in AlphaFold 3
- [Specifying Ligands and Modifications](https://mintlify.wiki/google-deepmind/alphafold3/advanced/ligands-and-modifications.md): Learn how to specify ligands using CCD codes, SMILES strings, and custom chemical components in AlphaFold 3
- [Running Pipeline in Stages](https://mintlify.wiki/google-deepmind/alphafold3/advanced/pipeline-stages.md): Learn how to run AlphaFold 3's data pipeline and inference separately for optimized resource utilization
- [build_data](https://mintlify.wiki/google-deepmind/alphafold3/api/build-data.md): Data preparation command for AlphaFold 3
- [Resources](https://mintlify.wiki/google-deepmind/alphafold3/api/common/resources.md): Utilities for loading external resources, tools, and data files
- [Chemical Components](https://mintlify.wiki/google-deepmind/alphafold3/api/constants/chemical-components.md): Chemical Components found in PDB (CCD) constants and utilities
- [Residue Names](https://mintlify.wiki/google-deepmind/alphafold3/api/constants/residue-names.md): Constants associated with residue names for proteins, RNA, and DNA
- [Featurisation Module](https://mintlify.wiki/google-deepmind/alphafold3/api/data/featurisation.md): Convert folding inputs into model-ready feature batches for AlphaFold 3 prediction.
- [MSA Processing](https://mintlify.wiki/google-deepmind/alphafold3/api/data/msa.md): Multiple sequence alignment tools and featurisation for evolutionary information extraction.
- [Template Processing](https://mintlify.wiki/google-deepmind/alphafold3/api/data/templates.md): Retrieve and process structural templates from PDB for template-based structure prediction.
- [folding_input.py](https://mintlify.wiki/google-deepmind/alphafold3/api/folding-input.md): Model input dataclasses for AlphaFold 3 structure prediction
- [model.py](https://mintlify.wiki/google-deepmind/alphafold3/api/model.md): AlphaFold 3 model architecture and inference results
- [Features](https://mintlify.wiki/google-deepmind/alphafold3/api/model/features.md): Data-side input feature processing for AlphaFold 3 model inputs.
- [Inference](https://mintlify.wiki/google-deepmind/alphafold3/api/model/inference.md): Core inference functions and result dataclasses for AlphaFold 3 model predictions.
- [Post-processing](https://mintlify.wiki/google-deepmind/alphafold3/api/model/post-processing.md): Post-processing utilities for AlphaFold 3 inference results and output file generation.
- [pipeline.py](https://mintlify.wiki/google-deepmind/alphafold3/api/pipeline.md): Data pipeline for MSA generation and template search
- [run_alphafold.py](https://mintlify.wiki/google-deepmind/alphafold3/api/run-alphafold.md): Main AlphaFold 3 structure prediction script and entry point
- [mmCIF Parsing](https://mintlify.wiki/google-deepmind/alphafold3/api/structure/mmcif.md): Utilities for parsing and manipulating mmCIF files
- [Structure](https://mintlify.wiki/google-deepmind/alphafold3/api/structure/structure.md): Core Structure class for representing and processing molecular structures
- [Data Pipeline](https://mintlify.wiki/google-deepmind/alphafold3/concepts/data-pipeline.md): MSA generation, template search, and feature processing in AlphaFold 3
- [Inference Pipeline](https://mintlify.wiki/google-deepmind/alphafold3/concepts/inference-pipeline.md): Detailed walkthrough of the AlphaFold 3 inference pipeline from input to structure output
- [Model Architecture](https://mintlify.wiki/google-deepmind/alphafold3/concepts/model-architecture.md): Deep dive into AlphaFold 3's neural network architecture and components
- [AlphaFold 3 Overview](https://mintlify.wiki/google-deepmind/alphafold3/concepts/overview.md): Comprehensive overview of AlphaFold 3 architecture, approach, and capabilities
- [Confidence Metrics](https://mintlify.wiki/google-deepmind/alphafold3/guides/confidence-metrics.md): Understanding pLDDT, PAE, pTM, and ipTM confidence scores
- [Database Setup](https://mintlify.wiki/google-deepmind/alphafold3/guides/database-setup.md): Setting up genetic and structural databases for AlphaFold 3
- [Input File Format](https://mintlify.wiki/google-deepmind/alphafold3/guides/input-format.md): Overview of AlphaFold 3 input JSON format and specifications
- [JSON Specification](https://mintlify.wiki/google-deepmind/alphafold3/guides/json-specification.md): Detailed specification for AlphaFold 3 input entities with examples
- [Output Format](https://mintlify.wiki/google-deepmind/alphafold3/guides/output-format.md): Understanding AlphaFold 3 output structure and files
- [Performance Optimization](https://mintlify.wiki/google-deepmind/alphafold3/guides/performance-optimization.md): Tips and techniques for optimizing AlphaFold 3 performance
- [Running with Docker](https://mintlify.wiki/google-deepmind/alphafold3/guides/running-docker.md): How to run AlphaFold 3 using Docker containers
- [Running with Singularity](https://mintlify.wiki/google-deepmind/alphafold3/guides/running-singularity.md): How to run AlphaFold 3 using Singularity containers
- [Installation Guide](https://mintlify.wiki/google-deepmind/alphafold3/installation.md): Complete installation instructions for AlphaFold 3 including Docker, GPU drivers, and genetic databases
- [AlphaFold 3 - Accurate Biomolecular Structure Prediction](https://mintlify.wiki/google-deepmind/alphafold3/introduction.md): Implementation of the AlphaFold 3 inference pipeline for predicting protein, RNA, DNA, and ligand structures with state-of-the-art accuracy
- [Model Parameters Terms of Use](https://mintlify.wiki/google-deepmind/alphafold3/legal/model-parameters-terms.md): Terms of use for AlphaFold 3 model parameters
- [Output Terms of Use](https://mintlify.wiki/google-deepmind/alphafold3/legal/output-terms.md): Terms of use for AlphaFold 3 output
- [Prohibited Use Policy](https://mintlify.wiki/google-deepmind/alphafold3/legal/prohibited-use-policy.md): AlphaFold 3 model parameters prohibited use policy
- [Source Code License](https://mintlify.wiki/google-deepmind/alphafold3/legal/source-code-license.md): Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License
- [Obtaining Model Parameters](https://mintlify.wiki/google-deepmind/alphafold3/obtaining-model-parameters.md): How to request access to AlphaFold 3 model parameters from Google DeepMind
- [Quick Start Guide](https://mintlify.wiki/google-deepmind/alphafold3/quickstart.md): Run your first AlphaFold 3 prediction with step-by-step examples
- [Citation](https://mintlify.wiki/google-deepmind/alphafold3/resources/citation.md): How to cite AlphaFold 3 in your research
- [Community Tools](https://mintlify.wiki/google-deepmind/alphafold3/resources/community-tools.md): Third-party tools and resources for AlphaFold 3
- [Frequently Asked Questions](https://mintlify.wiki/google-deepmind/alphafold3/resources/faq.md): Common questions about AlphaFold 3
- [Known Issues](https://mintlify.wiki/google-deepmind/alphafold3/resources/known-issues.md): Known issues and workarounds for AlphaFold 3
- [Troubleshooting](https://mintlify.wiki/google-deepmind/alphafold3/resources/troubleshooting.md): Common problems and solutions for AlphaFold 3