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!

Features:

* 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.

http://www.hyper.com/Products/HyperProtein/tabid/504/Default.aspx

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