NVIDIA NIM for MSA Search

MSA-Search

• Overview
  • Advantages of NIMs
• Prerequisites and Support Matrix for MSA Search NIM
  • Sequence Databases and Search Types
  • Supported Hardware
    • Minimum System Hardware Requirements
    • Supported NVIDIA GPUs
  • Software Prerequisites
  • NGC (NVIDIA GPU Cloud) Account
• Release Notes
  • Release 2.2.0
    • Summary
    • New Features
      • Structural Template Search
      • Case-Insensitive Database Names
    • Bug Fixes
      • Consistent Profile Generation Database Selection
      • Merged Alignment Now Includes All Requested Databases
    • Documentation
    • Deprecations
    • Migration Notes
  • Release 2.1.0
    • Summary
    • Key Changes
      • Paired MSA Search for Protein Complexes
      • API Changes
    • New Features and Improvements
  • Release 2.0.0
    • Summary
    • Key Changes
      • GPU Server Enabled by Default
      • Database Changes
      • MMSeqs2 Version Upgrade
      • Hardware Support
    • New Features and Improvements
    • Performance Enhancements
    • Migration Notes
      • Configuration Changes
      • Hardware Requirements
      • For Existing Users
  • Release 1.0.0
    • Summary
    • Model Variants
    • Notes and Limitations
• Getting Started
  • Prerequisites
  • Starting the NIM Container
  • MSA Search Examples
    • Python Client Example
    • Shell Client Example
  • Paired MSA Search for Protein Complexes
    • Python Client Example (Paired)
    • Shell Client Example (Paired)
  • Structural Template Search
    • Python Client Example (Template Search)
    • Shell Client Example (Template Search)
  • Next Steps
• Configuration
  • GPU Selection
  • Environment Variables
  • Volumes
• Task-Specific Profiles and Custom Databases
  • Task-Specific Profiles
    • Listing Available Profiles
    • Selecting a Profile
    • Available Profiles
  • Custom Databases
    • Prerequisites
    • Specifying Custom Databases
    • Example: Loading a Manually Downloaded Database
    • Available Databases
    • Database Directory Structure
    • Database Discovery
• Indexing Databases for GPU Server
  • When to Index
  • Using MMseqs2 from the NIM Container
  • Example: Re-indexing a Downloaded Database
    • 1. Download the database
    • 2. Examine the database files
    • 3. Remove existing index files
    • 4. Re-create the index for GPU Server
    • 5. Verify the index was created
  • MMseqs2 Command Reference
• Optimization and Scaling
  • Scaling and Load Balancing
• Benchmarking
  • Accuracy
    • Accuracy Metrics
      • AlphaFold2 Search - Database Coverage
      • ColabFold Search - Database Coverage
      • Paired MSA Search - Accuracy by Complex
  • Performance
    • Performance Metrics
      • AlphaFold2 Search Type (Iterative)
      • ColabFold Search Type (Cascaded)
      • Paired MSA Search (ColabFold Paired)
      • Structural Template Search
  • Sample Benchmarking Scripts
• Observability
  • Metrics
  • Telemetry
    • Benefits
    • Configuration
    • More Information
• API Reference
  • OpenAPI Specification
  • Multiple Sequence Alignment Search
    • Input Parameters
  • Paired Multiple Sequence Alignment Search
    • Input Parameters
    • Outputs
  • Structural Template Search
    • Input Parameters
    • Outputs
  • Get Database Configuration
    • Input Parameters
    • Outputs
  • Get MMSeqs2 Version
    • Input Parameters
    • Outputs
  • Health Endpoints
    • Readiness Check
      • Outputs
    • Liveness Check
      • Outputs
  • NIM Metadata Endpoints
    • Version
      • Outputs
    • License
      • Outputs
    • Metadata
      • Outputs
    • Manifest
      • Outputs
    • Metrics
      • Outputs