RESMAP

Resmap: Automated representation of macromolecular interfaces as two-dimensional networks

Liskin Swint-Kruse* and Curtis S. Brown. 
Department of Biochemistry and Molecular Biology,
The University of Kansas Medical Center, Kansas City, KS 66160

Download: RESMAP License
Contact: lswint-kruse@kumc.edu   Suggestions for updates are welcome.

Program goal:  Re-cast noncovalent protein-protein or protein-DNA interactions as networks, to aid comparison of homologuous structures

screenshot

Platforms available
Download executable to run on Windows 2000 and XP operating systems. 
Command-line executable available for Linux and Mac OS-10. 

Import files

*.pdb Atomic coordinates of protein structure
*.rcf   Atom-type and interaction definitions
Default supplied with program download (protein and DNA)
May be changed by user, additional molecules may be added to definitions
*.aln Sequence alignment to compare 2 homologues (within Diff window)
Example provided with program download


Resmap calculations
Automatically calculates
All atom-atom distances between two chosen residue ranges
Generates networks (shown above)
Interactively alter cutoff distances for each interaction type (left side of screen shot)
Tools/Diff:  Compare 2 networks within Resmap, plot difference and/or intersection network (ex. below)

screenshot

screenshotExport files
*.ps *.eps
Network pictures to import into graphics programs for modification (line width, color, font size - see figure at right).  Variables (e.g. cut-off distances, definition filename) can be viewed when opened as text files

*.raw
Text file with interacting atoms and shortest distance

Example uses:

  • Compare structures of homologues (Swint-Kruse et al. 2001; Swint-Kruse et al. 2002)
  • Compare structure “snapshots” during molecular dynamics simulations (Swint-Kruse et al. 2002)
  • Compare structures of the same protein bound to different ligands (Swint-Kruse 2004)

 

General RESMAP Description/Citation:
Swint-Kruse, L. and C. S. Brown (2005). "Resmap: automated representation of macromolecular interfaces as two-dimensional networks." Bioinformatics 21(15): 3327-8.
Note:  Diff/Alignment inputs were added in a later release; documentation for these features is contained in the download page.

License agreement/request download.


REFERENCES

Swint-Kruse, L. (2004). "Using networks to identify fine structural differences between functionally distinct protein states." Biochemistry 43(34): 10886-95.

Swint-Kruse, L. and C. S. Brown (2005). "Resmap: automated representation of macromolecular interfaces as two-dimensional networks." Bioinformatics 21(15): 3327-8.

Swint-Kruse, L., C. R. Elam, et al. (2001). "Plasticity of quaternary structure: Twenty-two ways to form a LacI dimer." Protein Sci. 10: 262-276.

Swint-Kruse, L., C. Larson, et al. (2002). "Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR." Protein Sci 11(4): 778-94.

Last modified: Jun 13, 2014
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