Scp


Introduction

runLagrange [1] is a tool that computes provably optimal solutions to the side-chain placement problem.

Note

warning runLagrange needs to be linked dynamically with BALL 1.2

Quick Start

Usage:
./runLagrange  [-nopreproc]  [-novarprune]  <lb>|-nolb  <energies_file>

[-nopreproc]

By default the following preprocessing is applied to decrease the size of the problem instance while preserving optimality: (i) Goldstein DEE (see [11] in the paper) (ii) Residue reduction (see [26] in the paper) This preprocessing can be disabled by the option -nopreproc

[-novarprune]
Furthermore, rotamers that can be proven by the initial primal bound to be suboptimal will be eliminated. Option -novarprune disables this elimination.

<lb>|-nolb
Either a primal (lower) bound is given or indicate with -nolb that no such bound is available.


References

[1] Canzar S, Toussaint NC, Klau GW. An exact algorithm for side-chain placement in protein design. Optim Lett, to appear 2011.


Download

Our development platform is 64 bit Linux. We do not support other platforms. If you are interested in compiling the code on your own to run it on other platforms please contact the authors.

Compiled with g++ (GCC) 4.1.2 for Linux-x86 64 bit.

version date link comment
1.0 March 2011 runLagrange 1.0 Version used for the computations in [1]

data date comment
instances March 2011 In [1] we used two benchmark sets. We eliminate, in a preprocessing phase, residues of low degree and rotamers according to Goldstein's dead-end elimination theorem. For details we refer to the paper. All instances are available in the original as well as the preprocessed form upon request (data is too large to download).


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Topic revision: 18 Jul 2011, GunnarKlau