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 Agreement/Access Download Instructions
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
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
| File extension | Description |
|---|---|
| *.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)
Export 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/Access Download Instructions
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.