It can be challenge to find a software package that integrates all the necessary components for successful protein analysis. Understanding the structure of a protein is critical to understanding protein function, but many protein analysis tools miss the crucial connection between analysis of protein structure and biophysical properties of the protein sequence.

Lasergene Protein rises above other protein analysis tools by offering flexible, rich 3D graphical representations of protein structures, full integration with both sequence and structure analysis, protein design tools that allow you to effortlessly predict protein stability, and unmatched accuracy in predicting protein structures through integration with our Nova Applications.

Lasergene Protein Workflows

Antibody Modeling*

Use NovaFold Antibody to predict highly accurate antibody models from sequence data in minutes.

Antibody modeling is an important tool for antibody design and optimization and accuracy is paramount. Many antibody modeling tools rely solely on homology modeling, but NovaFold Antibody’s unique algorithm generates models of antibodies and antibody fragments by combining homology modeling for framework regions and fragment-based or ab initio modeling for hypervariable loop regions, resulting in highly accurate antibody structure predictions. Simply provide sequences for the light chain, the heavy chain, or both, and NovaFold Antibody will return an annotated report that includes the predicted antibody models, as well as the highest likelihood heavy chain and light chain templates and annotations for locations of CDR loops. Easily view antibody modeling results with annotations in Protean 3D, part of Lasergene Protein, which allows you to fully customize the rendering to aid in visualization, or to prepare publication-quality images to export. Antibody modeling with NovaFold Antibody can also be used in conjunction with NovaDock to predict the structure and binding of antibody-antigen complexes.

Epitope Prediction

Use Protean 3D to accurately perform B-cell epitope prediction using only sequence-based information.

B-cell epitopes–the part of an antigen recognized by an antibody–are conformational in nature; however, accurate epitope prediction is difficult for proteins without a known 3D structure. Protean 3D, part of Lasergene Protein, uses a machine learning approach that improves the ability to perform B-cell epitope prediction using only sequence-based information, providing better overall predictive accuracy than other leading epitope prediction methods. Protean 3D enables you to view predicted epitopes and antigenic regions along your sequence and structure, and compare predictions to other characteristics, such as surface probability. Easily 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, and change the appearance of predicted epitopes on the sequence and structure for optimized visualization and publication-quality images.

Protein Docking*

NovaDock explores protein flexibility when docking, resulting in more accurate protein-protein interaction predictions.

Modeling a protein-protein docking interaction is generally more difficult than predicting the structure of an individual protein, and because of its complex nature, accuracy can be a concern. NovaDock offers the ability to predict protein-protein docking interactions for any two binding partners utilizing SwarmDock, one of the top algorithms validated in the CAPRI blind docking experiment. Utilizing the SwarmDock algorithm, NovaDock explores protein flexibility when docking, resulting in more accurate predictions. Simply provide your ligand and receptor PDB or structure files, proposing specific residue contacts between the binding partners if desired. NovaDock will then predict the three-dimensional structure of the multiprotein complex and provide energy score, cluster size, and number of ligand contacts for each model for analysis.

Protein Sequence Analysis

Use Protean 3D for comprehensive protein sequence analysis in one easy-to-use application!

Protein sequence analysis is essential for studying and predicting protein function and structure, but often protein sequence analysis tools lack the visualization component necessary for interpretation, or they require additional tools for downstream analysis. The protein sequence analysis tools available in Protean 3D provide elegant graphical representations of the applied methods, making it simple to analyze biophysical properties, predict secondary structures such as B-cell epitopes, calculate surface probability, perform amino acid composition analysis, and more. What’s more, Protean 3D is a complete protein sequence analysis software package, meaning that after you analyze and annotate your protein sequence, you can immediately perform protein structure analysis, as well as predict protein structure, perform antibody modeling, or evaluate protein-protein docking interactions. Use Protean 3D to have everything you need for comprehensive protein sequence analysis in one easy-to-use application!

Protein Stability Prediction

Use Lasergene Protein’s protein design software to perform essential protein stability predictions in minutes.

Protein stability prediction is essential for optimizing protein functional studies, but many standard approaches to improving solubility and expression are often ineffective due to degradation or thermodynamic instability. Our protein design software, part of Lasergene Protein, includes protein mutation stability prediction tools that use a deterministic protein design algorithm find the global minimum energy conformation (GMEC). This allows you to make changes at the residue-level on a protein structure and predict whether these changes are likely to be stabilizing or destabilizing compared to the original structure, a beneficial process for PCR site-directed mutagenesis. Our protein stability prediction tools also make it easy to search for amino acid positions that are important for protein stability by performing computational alanine scanning or serine scanning to detect hot-spots, residues whose variants destabilize the structure. Use Lasergene Protein’s advanced protein design software to perform accurate protein stability predictions in minutes!

Protein Structural Alignment

Use Protean 3D to easily perform protein structural alignments of entire macromolecular structures or selected regions.

Homologous proteins often have similar structures. Protein structural alignment software can be a valuable tool for identifying these similarities by comparing the shape and 3D conformation between structures. Protein structural alignment is also a valuable tool for comparing NovaFold predicted models to template structures from the Protein Data Bank. Protean 3D, part of Lasergene Protein, makes it easy to identify regions of similarity between two or more structures, independent of sequence similarity. Simply add your structure files or open your NovaFold results, and select from the TM-Align or jFATCAT rigid-body alignment algorithms. Following your protein structural alignment, evaluate RMSD values for aligned structures to determine their divergence from one another. Then, customize the rendering of your visualization in Protean 3D to prepare your protein structural alignment image for publication.

Protein Structure Analysis

Use Protean 3D for complete protein structure analysis in one user-friendly application!

Understanding the structure of a protein is critical to understanding protein function, but many protein structure analysis tools available today lack the high-quality visualization component necessary for effective analysis and miss the crucial connection between analysis of protein structure and biophysical properties of the protein sequence. Protean 3D, part of Lasergene Protein, removes these challenges by creating beautiful, flexible, rich graphical representations of your protein and providing full integration with protein sequence analysis and structure prediction tools in a single application. Our protein structure analysis tools make it effortless to analyze your protein structure for regions of interest or to introduce a mutation and see the impact on the protein structure. Infinite possibilities for visualizing the three-dimensional protein structure provide an uncomplicated means of producing publication-quality images. Use Protean 3D to have everything you need for comprehensive protein structure analysis in one user-friendly application!

Protein Structure Prediction*

Create highly accurate protein models, unattainable through standard modeling methodologies.

Protein 3D structure prediction from a unique amino acid sequence is so important because having a protein structure model provides a greater level of understanding of how a protein works, which can allow us to create hypotheses about how to affect it, control it, or modify it. Many tools for protein structure prediction rely solely on homology modeling, which only works well for proteins that have a high degree of sequence similarity to protein sequences in the Protein Data Bank.

By contrast, NovaFold and NovaFold AI use two different award-winning algorithms to create highly accurate, full 3D atomic models of proteins that are unattainable through standard modeling methodologies.

NovaFold utilizes the award-winning I-TASSER protein structure prediction algorithm, which combines threading and ab initio folding technologies. NovaFold finds more distant relationships than sequence similarity alone, improving the quality and accuracy of the predicted structure.
NovaFold AI uses the AlphaFold 2 algorithm from DeepMind, winner of the most recent CASP14 challenge, to predict distance and create dihedral maps using deep multiple sequence alignments as input. This algorithm does not directly use templates to place atomic coordinates but can use templates as part of the map building process.

Lasergene Protein Applications

Protean 3D

Protein Sequence and Structure Analysis

Protean 3D offers flexible, rich 3D graphical representations of protein structures, incorporating both sequence and structure analysis as well as protein stability prediction tools.

NovaFold*

Protein Structure Prediction

NovaFold is protein structure prediction software that works with Lasergene Protein to build accurate, full 3D atomic models of proteins with previously unknown structures.

NovaFold Antibody*

Antibody Modeling

NovaFold Antibody software generates highly accurate models of antibodies and antibody fragments utilizing a combination of homology modeling and ab initio loop prediction.

NovaDock*

Protein-Protein Docking

NovaDock is a high-resolution protein-protein docking application that predicts atomic interactions between any two proteins.

Compare DNASTAR Lasergene Packages

	Lasergene Molecular Biology	Lasergene Genomics	Lasergene Protein	DNASTAR Lasergene MOST POPULAR
Included Applications
SeqBuilder Pro	√			√
SeqMan Ultra	√	√		√
MegAlign Pro	√			√
GeneQuest	√			√
GenVision	√			√
SeqNinja	√			√
SeqMan NGen		√		√
ArrayStar		√		√
GenVision Pro		√		√
Protean 3D (+1 prediction per Nova Application)			√	√
DNASTAR Navigator	√	√	√	√

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