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Comparison of a list of structures with 2-tandem C2H2 type zinc finger domains in automated mode

• Job home: Zinc finger domains: automated mode
• Flexible structure alignment: 2 domains are aligned
• Rigid structure alignment: no alignment
• Screen short gallery (click on image for larger view):

  Flexible Alignment	Flexible Common Core	Rigid Alignment	Rigid Common Core

Comparison in user-guided mode by specifying one zinc finger domain in each structure when comparison in automated mode fails

• Job home: Zinc finger domains: specifying the 1st zinc finger domain in each structure
• Rigid structure alignment: aligned on 1st zinc finger domain in all structures
• Screen short gallery (click on image for larger view):

  Rigid Alignment without DNA	Rigid Common Core without DNA	Rigid Alignment with DNA	Rigid Alignment of protein-DNA complexes

Comparison in user-guided mode by specifying one zinc finger domain in only one structure (reference) when comparison in automated mode fails

• Job home: Zinc finger domains: specifying the 1st zinc finger domain in one structure
• Rigid structure alignment: aligned on 1st zinc finger domain in all structures
• Screen short gallery (click on image for larger view):

  Rigid Alignment with DNA	Rigid Alignment without DNA	Rigid Alignment of protein-DNA complexes

Comparison of a list of Calmodulin domains

• Job home: Calmodulin
• Flexible structure alignment: whole protein domain structures are aligned
• Rigid structure alignment: only one subdomain was aligned
• Screen short gallery (click on image for larger view):

  Flexible Alignment	Rigid Alignment

Comparison of HIV virus antiboby and antigen complexes

• Comparison of two antibody-antigen complexes of HIV viruses
• Comparison based on the antigen chains of 2ny7, 3u7y: the antibody heavy chains and light chains are in different angle with the antigen chains
• Comparison based on the heavy chains of 2ny7, 3u7y: the antigen chains are in different angle with the antibody chains
• Screen short gallery (click on image for larger view):

  Comparison on the Antigen Chains	Comparison on the Heavy Chains

• Comparison of three antibody-antigen complexes of HIV viruses
• Comparison based on the antigen chains of 3ngb, 4j6r and 4jm2: the antibody heavy chains and light chains are in different angle with the antigen chains
• Screen short gallery (click on image for larger view):

  Comparison on Antigen Chain	Common Core on Antigen Chain

Comparison of motifs or domains within one protein structure

• Compare 3 RRM domains within protein 3smz chain A
• Job home: 3smz: a 3-RRM domain protein structure
• Rigid structure alignment: 3 RRM domains are aligned
• Screen short gallery (click on image for larger view):

  Rigid Alignment	Rigid Common Core

Comparison of a list of 1-RRM domain protein structures with different RNA positions

• Job home: 1-RRM domain protein structures complexed with RNA molecules
• Rigid structure alignment: it allows users to view 1-RRM domain structures complexed with RNA molecules.
• Screen short gallery (click on image for larger view):

  Rigid Alignment with RNA	Rigid Common Core with RNA	Rigid Alignment without RNA

Comparison of a list of 2-RRM domain protein structures complexed with RNA molecules

• Job home: 2-RRM domain protein structures complexed with RNA molecules.
• Flexible structure alignment: 2 RRM domains are aligned
• Rigid structure alignment: only 1 RRM domain from each structure is aligned. Allow to view RNA molecules.
• Screen short gallery (click on image for larger view):

  Flexible Alignment	Flexible Common Core	Rigid Alignment	Rigid Common Core	Rigid Alignment without RNAs

Using experts knowledge to compare a list of protein structures when automated structure comparison fails

• Automated structure comparison failed for a list of RRM domain proteins: 1fje, 1cvj, 1yty, 2adc, 3sde, 3smz, 2kxf, 2yh0
  • Job home: structurally diverse RRM domain protein comparison
  • Rigid structure alignment: no residues were found structurally in common
  • Screen short gallery (click on image for larger view):

    Rigid Alignment	Rigid Common Core

• Use expert knowledge of all structures and run POSA multiple structure alignment again
  • Job home: use expert knowledge to analyze domain-domain interaction differences of a list structurally diverse 2-RRM domain protein structures
  • Rigid structure alignment: One RRM domain (βαββαβ) are aligned from all structures.
  • Screen short gallery (click on image for larger view):

    Rigid Alignment	Rigid Common Core	Rigid Alignment without RNAs

Comparison of a list of tRNA synthetase proteins and their complexes

• Job home: tRNA synthetase
• Flexible structure alignment: one more domain was aligned than with rigid structure alignment.
• Rigid structure alignment: it allows users to view tRNA synthetases complexed with other molecules.
• Screen short gallery (click on image for larger view):

  Flexible Alignment	Flexible Common Core	Rigid Alignment	Rigid Common Core

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