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HyperProtein 化學計算軟體​​​

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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.


HyperProtein 是 Hypercube, Inc 的產品,可用於蛋白質序列相關的計算科學。該產品包括一維蛋白序列的分析,以及三維蛋白質結構的分析。序列和結構之間的關係更是該產品的一個強項。不像其他軟體只能單獨用於蛋白質序列或結構,他另外還提供了序列比對的功能。

HyperProtein 將蛋白質模擬推至一個全新的水平。利用圖形,分子力學,以及各種分子建模功能,HyperProtein 轉換世界三維建模的世界,讓分子模擬容易地操控。

HyperProtein 始於一個序列或一組蛋白質家列。也就是說,它操縱和分析不同種類的家族同源蛋白質。它針對這些序列,建立供種的系統樹,並生成序列樹中的源頭。然後,它可以讓您沿著它探索、探討三維蛋白質與家族結構的變化和進化分支的差異。

序列的蛋白質結構先驗預測問題尚未解決,HyperProtein 已可協助您探索此重要問題。它採用神經網絡,從序列預測二級結構。它允許任何結構、任何大小的分子力學的優化。結合序列分析和分子模擬從序列產生可用的蛋白質三維結構。

特色:

  • 多窗口應用程序,允許項目和圖形用戶界面的方法來執行生物信息學和系統發育。
  • 生物信息連接到分子模型。
  • HyperChem 中與蛋白質相關的所有功能都包含在 HyperProtein。
  • 各種操作、分析、蛋白質序列的顯示器。
  • 蛋白家族的多序列分析 (MSA)。
  • 分析演化改變的蛋白質序列及其三維結構。
  • 從初級序列預測二級結構。
  • 序列和它們的性質的綜合圖形分析。

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