PROTEIN ANALYSIS AND STRUCTURE PREDICTION WORKFLOWS

Analysis and Modeling Tools for Protein Data

Lasergene Protein is a robust set of tools for protein sequence analysis, macromolecular visualization, and protein structure prediction and analysis. The foundation of Lasergene Protein is Protean 3D, which is used to explore macromolecular structure, motion, and function. Lasergene Protein can be used with our Nova Applications, for protein structure prediction and modeling.

Sequence and Structure Analysis

Protein Modeling

Benchmarks

Protein Sequence and Structure Analysis

Lasergene Protein includes Protean 3D, our application for protein sequence and protein structure analysis. Using the integrated views within the software, you can view macromolecular sequence, structure and prediction methods simultaneously.  Sequences and structures can be annotated and exported to PDF, bitmap and PowerPoint formats.

Protein Sequence Analysis

  • Import protein structure or sequence files from GenBank and PDB
  • Analyze biophysical properties such as amphilicity, charge density, disorder, flexibility, hydropathy, and stability
  • Access to multiple methods for secondary structure prediction
  • Calculate surface probability and predict probable transmembrane regions
  • Perform amino acid composition analysis for selections or full proteins
  • Create and manage features and annotations
  • Translate or batch translate DNA sequences in SeqBuilder Pro
  • Export to PDF, bitmap and PowerPoint formats

Protein Structural Analysis

  • Import protein structure or sequence files
  • Download PDB files directly from the Protein Data Bank or import multi-model PDB files to view conformational changes.
  • Utilize integrated protein sequence analysis tools to highlight regions of interest on the protein structure
  • Introduce a sequence mutation and see the impact on the protein structure
  • Change the rendering, orientation and lighting on a structure
  • Browse and search over 300 animated and annotated macromolecular conformational changes calculated by the Yale Morph Server
  • Export movie files from protein structures and animations

Epitope Prediction

  • Predict B-cell epitopes and antigenic regions based on protein sequence data
  • Compare epitope predictions to other characteristics, such as surface probability
  • Create molecular and solvent accessible surfaces around your structure and view predicted epitopes relative to the protein surface
  • View confidence scores for predicted antigenic regions
  • Change appearance of predicted epitopes on the sequence and structure for optimized visualization

Structural Alignment

  • Align entire macromolecular structures or selected regions
  • Identify regions of similarity between two or more structures, independent of sequence similarity
  • View RMSD values for aligned regions
  • Visualize aligned structures in the Structure View
  • Export images of aligned structures

Molecular Motion Visualization

  • Browse and search over 300 animated and annotated macromolecular conformational changes calculated by the Yale Morph Server
  • Access to detailed information for each animation model, including links to molecule information in the PDB, CATH, and GO databases
  • Effortlessly slow and pause animation to interrogate protein models
  • Compare selected animations by overlaying models
  • Export molecular motion animations as QuickTime movies, AVI format, or animated GIF

SNP to Structure Analysis

Protein Structure Mutation Model
  • Combine genomic sequencing and SNP analysis results with structure files from the PDB to model point mutations on the protein structure and assess the effect on protein stability.
  • Model SNPs of interest in Protean 3D and view the mutated amino acid side chains along the backbone
  • Use DFIRE energy calculations to predict whether the mutation is stabilizing or destabilizing to the protein structure
  • Apply solvent-accessible surfaces to further explore potential impact of mutation on protein stability and function
  • Analyze secondary structure characteristics to interrogate mutation’s effect on protein flexibility, amphiphilicity, charge density, hydropathy, and more

Note: The use of this workflow requires assembly with the Homo sapiens – Ensembl w/PDB genome template package.

Protein Modeling

Our protein modeling tools generate highly accurate structural models of both proteins and protein-protein complexes that are unattainable through standard modeling methodologies. Our Nova Applications for protein structure prediction, antibody modeling, and protein-protein docking are available as optional, cloud-based applications when you purchase Lasergene Protein. We always include one prediction for each Nova app when you buy, so that you can try our protein modeling capabilities for free. And our protein design tools are included free of charge with each academic, government and non-profit license.

Protein Structure Prediction with NovaFold

  • Predict accurate, 3D atomic models of proteins, using a combination of threading and ab initio protein structure prediction technologies
  • View protein models in the integrated Protean 3D views
  • Analyze protein prediction results using a variety of statistics, including TM-score, RMSD, C-score, and more
  • Predict protein-ligand binding sites and protein function
  • Align similar experimental structures with predicted NovaFold models
ACCESS NOVAFOLD ON THE CLOUD

Antibody Modeling with NovaFold Antibody

  • Generate models of antibodies and antibody fragments (Fv, Fab, VH, sdAb)
  • Provide sequences for the light chain, the heavy chain, or both
  • Search a library of antibody frameworks, or provide custom templates
  • Automated annotation of CDR loops
  • View prediction results in Protean 3D for further structure analysis and rendering, and to export publication-quality graphics
  • Use with NovaDock to predict the structure and binding of antibody-antigen complexes
ACCESS NOVAFOLD ANTIBODY ON THE CLOUD

Protein Design

  • Scan for “hot-spots” using alanine and serine scanning to locate residues that are important for protein fold stability.
  • Create specific variants and see how they impact changes in energy.
  • Utilize the protein design tools in Protean 3D in combination with the virtual cloning and primer design capabilities in SeqBuilder Pro when performing PCR site-directed mutagenesis to see the structural impact of a mutation before designing your primers.

Protein Docking with NovaDock

  • Predict protein docking interactions for two binding partners in NovaDock, which utilizes SwarmDock, one of the top three algorithms validated in the CAPRI blind docking experiment
  • Provide your ligand and receptor sequence files, and propose specific residue contacts between the binding partners, if desired
  • Evaluate energy score, cluster size, and number of ligand contacts for each model in a summarized view, and adjust the filtering scheme as desired
  • Open any model as a new structure document for further exploration and to export custom images for publication
ACCESS NOVADOCK ON THE CLOUD
NovaFold Protein Structure Prediction Runtimes

*NovaFold runtimes plotted by sequence length and colored by TM-score

NovaFold Benchmarks

DNASTAR NovaFold was evaluated by recreating the CASP11 competition, in which participants attempted to predict the structures for a given set of target sequences whose structures were previously unknown. In this benchmark test, NovaFold created predictions for these same target sequences which were then evaluated and scored based on the same metrics used in the CASP11 experiment.

A normalized measure of similarity between superimposed protein structures weighs close atom pairs between structures greater than more distant atom pairs. The range varies from 0 to 1, with a higher score indicating a better structural match.

Additional Notes:

  • NovaFold versions 12.3 and higher support sequences up to 2,000 residues in length.
  • To accurately simulate the conditions of the original competition, the benchmark was run using a library composed only of templates available prior to the end date of the CASP11 contest. In addition, targets leaked during the competition were removed from the benchmark library.
  • This benchmark test utilized the Cloud-based version of NovaFold and evaluated structure prediction only, not binding or function prediction.

All of the functionality above is included in Lasergene Protein!

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