Structure Prediction Applications

While most of these applications focus on prediction, many have options which will also allow design.

Table of Contents

Ab initio modeling: Predict 3-dimensional structures of proteins from their amino acid sequences.
- Abinitio: Further documentation on the abinitio protocol
- NonlocalAbinitio: Application for predicting protein structure given some information about the protein's structure.
- Membrane abinitio: Ab initio for membrane proteins.
- Metalloprotein ab initio: Ab inito modeling of metalloproteins.
Backrub: Create backbone ensembles using small, local backbone changes.
Comparative modeling: Build structural models of proteins using one or more known structures as templates for modeling.
Floppy tail: Predict structures of long, flexible N-terminal or C-terminal regions.
Fold-and-dock: Predict 3-dimensional structures of symmetric homooligomers.
Molecular replacement protocols: Use Rosetta to build models for use in X-ray crystallography molecular replacement.
- Prepare template for MR: Setup script for molecular replacement protocols.
Relax: "Locally" optimize structures, including assigning sidechain positions.
RNA : see below for apps, including FARFAR & ERRASER (crystallographic refinement).
RosettaNMR with Paramagnetic Restraints: Structure prediction in RosettaNMR using backbone chemical shifts and paramagnetic restraints derived from metal ion tags.
trRosetta: Fragment-free structure prediction using constraints generated from sequence or multiple sequence alignment, and the power of deep neural networks. The #2 performer in the 2020 CASP14 competition, second only to AlphaFold2.

Loop modeling overview
CCD loop modeling: Sample loop conformations using fragments and the CCD closure algorithm.
Kinematic loop modeling: Sample loop conformations using the kinematic closure algorithm.
Next-generation KIC: A newer version of loop modeling with kinematic closure.
KIC with fragments: The latest version of loop modeling, combining kinematic closure with sampling of coupled degrees of freedom from fragments.
Loop closing: Closing chainbreaks introduced during modeling.
Stepwise assembly of protein loops: Generate three-dimensional de novo models of protein segments : Stepwise assembly of long loops: For loops greater than 4-5 residues. See also Stepwise monte carlo.
Stepwise monte carlo: Generate 3D models of protein, RNA, and protein/RNA loops, motifs, and interfaces. Stochastic version of stepwise assembly.

RNA structure prediction: Predict 3-dimensional structures of RNA from their nucleotide sequence. Read this first.
- RNA tools: Tools useful for RNA and RNA/proteinm including general PDB editing, cluster submission, job setup.
- RNA threading: Thread a new nucleotide sequence on an existing RNA structure.
- RNA motif prediction: Model RNA motifs with fragment assembly of RNA with full atom refinement (FARFAR).
RNA stepwise loop enumeration: Build RNA loops using deterministic stepwise assembly. See also Stepwise monte carlo.
Stepwise monte carlo: Generate 3D models of protein, RNA, and protein/RNA loops, motifs, and interfaces. Stochastic version of stepwise assembly.
RNA assembly with experimental constraints: Predict 3-dimensional structures of large RNAs with the help of experimental constraints. Note – largely deprecated by newer pipeline (documentation coming soon).
ERRASER: Refine an RNA structure given electron density constraints.
Sample around nucleobase: Visualizing energy functions by scanning probe molecules around a nucleobase.
RECCES: RNA free energy calculation with comprehensive sampling.
RNA pharmacophore: Extract and cluster the key features present in RNA (rings, hbond donors & acceptors) from the structure of a protein-RNA complex.

Antibody protocol (RosettaAntibody3): Overview of the antibody modeling protocol.
- Antibody Python script: The setup script.
- Grafting CDR loops: Graft antibody CDR templates on the framework template to create a rough antibody model.
- Modeling CDR H3: Determine antibody structures by combining VL-VH docking and H3 loop modeling.

See Also