PDBFixer
Fix common issues with PDB files such as missing atoms.
PDBFixer is a software tool used to prepare and repair protein structure files for molecular simulations. It addresses common issues with Protein Data Bank (PDB) files, such as missing atoms, missing residues, and improper formatting. PDBFixer can identify these problems and automatically correct them, making the protein structures suitable for computational analyses like molecular dynamics simulations. The tool is particularly useful for ensuring that PDB files are accurate and complete before they are used in various computational chemistry and Antibody Design applications.
Estimated resource cost: 0.00007238499999999999
Categories: Utilities & Conversions
Tags: Proteins Structure Fixing
Key Capabilities
- Hydrogen Addition: Automatically adds missing hydrogen atoms to protein structures, essential for molecular simulations.
- Heavy Atom Completion: Identifies and fills in missing heavy atoms, including those in flexible regions that are often unresolved in crystallographic data.
- Terminal Atom Fixes: Ensures terminal atoms at the ends of chains are present.
- Nonstandard Residue Handling: Removes nonstandard residues added for crystallographic purposes that are not part of the natural molecule.
- Selective Simulation Components: Allows users to exclude unwanted components such as salts, ligands, or multiple protein copies, focusing the simulation on the desired molecule.
- Multiple Location Resolution: Handles cases where multiple locations are listed for some atoms, ensuring a single, accurate representation.
- Automated Corrections: Fully automated process for fixing common issues in PDB files, saving time and reducing manual errors.
- Explicit Solvent Addition: Adds a water box around the structure for simulations in explicit solvent environments.
- Lipid Membrane Addition: Facilitates the addition of lipid membranes for simulations involving membrane proteins.
- Ease of Use: User-friendly interface and straightforward commands make it accessible for users with varying levels of expertise.
Runtime Statistics
| Metric | Value |
|---|---|
| runtime_mean | 34 |
| runtime_median | 3 |
| runtime_std | 221 |
| runtime_90th_percentile | 19 |
| runtime_max | 9718 |
Similar Tools
- PDB2PQR
- ClusterProt
- Foldseek Structural Clustering
- Kluster
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Review your configuration, then confirm the estimated credit cost before you run the job. Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: 0.00007238499999999999
Invite-only, limited-time access. Please contact ztang@getantibody.com.
Invite-only, limited-time access. Please contact ztang@getantibody.com.