REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES - DESIGN OF HYDROLYTICALLY-STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE.

Abbenante, G; March, D.R; Bergman, D.A; Hunt, P.A; Garnham, B; Dancer, R.J; Martin, J.L; Fairlie, D.P.

Structural Similarities for the Entities in PDB 1CPI

The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2].

To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

Currently viewing only significant results (P-value < 0.001). Show all available results.

Cluster data are up-to-date as of: Sep-27-2017

Info & Help Documentation

A detailed description of the procedure for the all vs. all alignments is available.

You can also use the structure comparison tool to compare any 2 given structures

Entity #1 | Chains A,B

Description: HIV-1 PROTEASE protein | Length: 99

No structure alignment results are available for 1CPI.A, 1CPI.B explicitly.

These chains are represented by chain 2HS1.A which has more than 70% sequence identity.

Show structure comparison results for representative 2HS1.A

Entity #2 | Chains C

Description: CYCLIC PEPTIDE INHIBITOR protein | Length: 6

This entity is too short to be considered for the all vs. all structure alignments.

References

[1] Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
Pre-calculated protein structure alignments at the RCSB PDB website
Bioinformatics 26: 2983-2985
[2] The all vs. all comparisons are based on jFATCAT (a Java port of the original FATCAT algorithm Yuzhen Ye & Adam Godzik (2003))
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Bioinformatics vol.19 suppl. 2. ii246-ii255.

[3] Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2008).
Data growth and its impact on the SCOP database: new developments.
Nucl. Acids Res. 2008 36: D419-D425
[4] Alexandrov N., Shindyalov I. (2003)
PDP: protein domain parser.
Bioinformatics 2003 Feb;19(3);429-30.

141209 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1CPI

REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES. DESIGN OF HYDROLYTICALLY STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE

Structural Similarities for the Entities in PDB 1CPI

Info & Help Documentation

No structure alignment results are available for 1CPI.A, 1CPI.B explicitly.

This entity is too short to be considered for the all vs. all structure alignments.

References

Prepare Data

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141209 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1CPI

REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES. DESIGN OF HYDROLYTICALLY STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE

Structural Similarities for the Entities in PDB 1CPI

Info & Help Documentation

No structure alignment results are available for 1CPI.A, 1CPI.B explicitly.

This entity is too short to be considered for the all vs. all structure alignments.

References