Use USalign Structural Alignment

Official Neurosnap webserver for accessing USalign Structural Alignment online.

Protein Design

Overview

US-align is a unified tool for comparing 3D structures of proteins, RNAs, and DNAs across various configurations (monomers, oligomers, and heterocomplexes) for pairwise and multiple alignments. It builds on TM-align, optimizing structural alignment through heuristic dynamic programming to maximize TM-score. Benchmark tests show that US-align achieves high accuracy with reduced CPU time compared to specialized alignment methods.

Neurosnap Overview

The USalign Structural Alignment online webserver allows anybody with a Neurosnap account to run and access USalign Structural Alignment, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • Performs 3D structure alignments for monomeric and complex structures of proteins, RNAs, and DNAs.
  • Utilizes a unified TM-score objective function for improved alignment accuracy and speed.
  • Optimized for fast and accurate alignment of complex oligomers and large macromolecular structures.
  • Includes a heuristic iterative searching algorithm to avoid local minima in alignments.

Statistics

Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.

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API Request

Access USalign Structural Alignment using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.

Job Note

Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.

Configuration & Options

Service Inputs

The input structure to use as the target structure.

The input structure to use as the reference structure.

Specify molecule types for alignment.

Select the structural alignment mode. Note: If you choose 'Alignment of two multi-chain oligomeric structures' under 'Alignment Type', set the 'Number of Chains to Align' to either 'Align all chains from all models' or 'Align all chains of the first model'.

Choose residue types for alignment. Default uses only ATOM records. HETATM option includes modified residues and ligands. MSE option includes selenomethionine residues.

Specify chain inclusion. Use 'Align all chains from all models' for biological assemblies and 'Align all chains of the first model' for asymmetric units.

Select the superposition method. The default performs sequence-independent alignment, while other options allow residue-based matching or sequence-dependent alignments, with complex structure options for multi-chain alignments. Note: If 'Superpose two complex structures by residue index and chain ID' or 'Superpose two complex structures with optimal chain mapping and TM-Score superposition' is selected for 'TM-Score Superposition,' set 'Number of Chains to Align' to either 'Align all chains from all models' or 'Align all chains of the first model.'

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