HyperProtein 1.0

Hypercube, Inc. announces the release of their newest product HyperProtein 1.0

HyperProtein is Hypercube, Inc.'s new product focusing on the computational science associated with protein sequences.  The product includes the analysis of one-dimensional protein sequences as well as the analysis of consequent three-dimensional protein structures.  In particular, the relationship between sequence and structure is a fundamental  facet of the product.  Unlike individual software programs that provide capability for some aspect of protein sequence or structure, such as sequence alignment, HyperProtein puts together a multitude of Bioinformatics and Molecular Modeling tools related to the science that initiates with a protein sequence.

HyperProtein brings protein simulation to a whole new level. Utilizing graphics, molecular mechanics, and various molecular modeling features, HyperProtein transforms the world of sequencing to a world of 3-dimensional modeling, putting molecular evolution at our fingertips.


HyperProtein starts with a sequence or a set of sequences representing a protein family.  That is,  it  manipulates and analyses a family of homologous proteins representative of different species.  It aligns these sequences, builds a phylogenetic tree for the species and generates the sequences for the ancestral species in the tree.  It then allows you to explore the differences along an evolutionary branch of  the tree including exploring the changes in a three dimensional protein structure representative of the protein family.  Do changes to protein structure from mouse to human occur on the surface, at the active site, etc? How does evolution affect the 3D functionality of proteins?


While the global problem of a priori prediction of protein structure from sequence is unsolved, HyperProtein allows exploration of this important problem.  It uses neural nets to predict secondary structure from sequence.  It allows molecular mechanics optimization of any structure large or small.  It generates a candidate 3D structure of a protein from sequence when the structure of a homologous protein is available. Combine sequence analysis and molecular modeling!

  • Multiple sequence alignment (MSA)
  • Profile alignment
  • Creation of ancestral sequences
  • Phylogenetic Tree generation and display
  • Mapping of phylogenetic tree to structure
  • Various colorings of sequences and mappings
  • Perl scripting and TCL scripting support
  • Rich project approach and windowing
  • Prediction of secondary structure
  • Homology
  • Mapping of MSA properties to structure

Click on a screenshot below to see HyperProtein's interface...


  • Multi-Windowed application that allows a Project and GUI approach to Bioinformatics and Phylogenetics.
  • Connection of Bioinformatics to Molecular Modeling.
  • All the features of HyperChem that are relevant to proteins are included in HyperProtein.
  • Various manipulations, analyses, and displays of protein sequences.
  • Multi-sequence analysis (MSA) of protein families.
  • Creation and display of evolutionary changes in proteins via phylogenetic trees created from MSAs.
  • Analysis of three-dimensional consequences of evolutionary changes occuring in protein sequences.
  • Direct connection between protein sequence changes and 3D changes in representative protein structures.
  • Prediction of secondary structure from primary sequence.
  • Integrated graphical analysis of sequences and their properties