HyperProtein Professional 1.0

Focuses on analyzing both one-dimensional protein sequences and their corresponding three-dimensional structures.

Explores the fundamental connection between protein sequence and its resulting 3D structure.

Combines multiple Bioinformatics and Molecular Modeling tools related to protein sequence analysis.

Uses graphics, molecular mechanics, and molecular modeling to transform sequence data into 3D models.

Works with sets of homologous protein sequences representing different species.

Aligns protein sequences to identify conserved regions and evolutionary relationships.

Creates phylogenetic trees from MSAs to visualize evolutionary relationships between species.

Generates the sequences of ancestral species within the phylogenetic tree.

Enables exploration of sequence and structural differences along specific branches of the evolutionary tree.

Allows users to investigate how changes in protein structure from one species to another (e.g., mouse to human) affect areas like the protein's surface or active site.

Provides tools to explore the prediction of protein structure from sequence, even though a priori prediction is a complex, unsolved problem.

Predicts secondary structure (e.g., alpha-helices, beta-sheets) from the primary sequence using neural networks.

Allows optimization of protein structures, both large and small, using molecular mechanics calculations.

Generates a candidate 3D structure of a protein from its sequence, based on the known structure of a homologous protein.

Provides a user-friendly interface with a project-based approach and graphical tools.

Integrates features from HyperChem (another product likely from Hypercube, Inc.) that are relevant to protein analysis.

Offers a range of tools for working with and visualizing protein sequences.

Directly links changes in protein sequences to their corresponding changes in 3D protein structures.

Provides graphical tools for analyzing sequences and their associated properties.