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		LIBRA I

LIBRA is the name of a computer application for analyzing protein structures and sequences. The basic methodology used is "Threading", which means that LIBRA evaluates the compatibility of a protein structure and a sequence. LIBRA I is the abbreviation for "LIght Balance for Remote Analogous proteins, ver. I". This page offers an interface to access LIBRA.

• Structural library was enlarged (3596 structures).
  

Functions

• Stability Analysis of Mutant Proteins using 3D Profiles

  To estimate the compatibility of protein structure and sequence, LIBRA employs the 3D profile instead of the 3D structure. The energy transfer of an amino acid from the denatured state to the native environment of the folding state is estimated at every site, using the simple pseudo-energy potential, and tabulated in the 3D profile.

• Structure Prediction by Threading: Forward Folding Protocol

  Compatible structures of a target sequence are sought from the structural library chosen from Protein Data Bank (PDB). The target sequence and 3D profile are aligned by simple dynamic programming. According to the alignment, sequence re-mounts on the structure and its fitness are evaluated by psuedo-energy potential. Scores are sorted from the best match and shown as well as their alignments.

• Sequence Homology Search by Threading: Inverse Folding Protocol

  Compatible sequences of a target structure are sought from the sequence database (Swiss-Prot). Scores are sorted from the best match and shown as well as their alignments. A recent study revealed that it is suitable in this search to use the 3D-1D alignment score per se as the compatibility score rather than the sequence re-mounting score.

References

• M. Ota, T. Mizunuma and K. Nishikawa (1997) Introduction to LIBRA (In Japanese). DDBJ off-line news. No.8.

• M. Ota, and K. Nishikawa (1999) Feasibility in the inverse protein folding protocol. Protein Sci. 8, 1001-1009

• M. Ota, Y. Isogai and K. Nishikawa (1997) Structural requirement of highly-conserved residues in globins. FEBS Lett. 415, 129-133

• M. Ota and K. Nishikawa (1997) Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins. Prot. Engng. 10, 339-351

• M. Ota, S. Kanaya and K. Nishikawa (1995) Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H. J. Mol. Biol. 248, 733-738

Diary

• 08/2/2002: Structural library was enlarged (3596 structures).
• 24/1/2001: Structural library was enlarged (2911 structures).
• 15/3/1999: Inverse folding search system was released.
• 10/9/1998: Structural library was enlarged, that includes about 1,400 structures.
• 10/9/1998: E-mail answer style of the forward folding search was improved.
• 12/1/1998: Some bugs in the forward folding search system were fixed.
• 2/10/1997: Forward folding search system was released.

Links

• National Institute of Genetics (NIG)

• Center for Information Biology (CIB)

• Laboratory for Gene-Product Informatics