LSim

Table of Contents

Overview

LSim superposes macromolecular electron densities and computes a structural similarity score. LSim computations scale linearly with the size of the molecules being compared.

The LSim alignments are conceptually unrelated to biochemical structural elements and, therefore, are unbiased and appropriate for structure-only protein similarity studies.

LSim: Electron density protein alignment

Input Command File

LSim is invocated trough a shell comand:

lsim job.cmd

A command file job.cmd looks like:

/gscan /bpdb /verbose /nmax=10
1MBS.pdb
1SCT.pdb

The first line is the command line. The following lines are the PDB file entries, one per line. A blank line indicates the command file termination. A .cmd extension is always assumed.

LSim commands

/gscan Scans Similarity function for a global maximization. When disabled a local maximization starts at LSim standard orientation.

/bpdb Forces reading B temperature factors from PDB files. When disabled or when B is read as zero, the standard B factor from lsim.par is used instead.

/verbose Extra printing.

/nmax or /nmax=n Performs nmax local optimizations at the best scanned orientations. Note that higher nmax values enhance global optimization, though it increases the computational cost. Non-repeated multiple maxima are printed.


Additional LSim parameters are located at the lsim.par file. Their modification, however, is discouraged. The LSim parameters are:

vcut Accuracy threshold for atom-atom similarity.

bfac Standard B factors.

matdir Number of director atoms in CAC global search.

maxiter Maximum iterations.

Outputs

LSim processes the job comand file, e.g. job.cmd, and outputs to a file named job.out. The output files look like:

---------------------------------------------------------------------------------
  LSIM LOG FILE
  LSim v 1.0, (C) Pere Constans 2001
  A Quantum Macromolecular Similarity Program
---------------------------------------------------------------------------------

Processing job.cmd

/gscan /Bpdb /nmax=10

Molecular Files Processing
Mol 1MBS  Nat=   1223  Zaa=   6185.77  Bn=  30.0  Bx=  30.0  Bm=  30.0  Dc=  5.38
Mol 1SCT  Nat=   1134  Zaa=   6953.30  Bn=  11.5  Bx=  50.3  Bm=  23.2  Dc=  6.12

Macromolecular Similarity Processing

Pair Similarity  Z(1MBS,1SCT)
Visualization files:     ls_1MBS.pdb   ls_1MBS_1SCT.pdb   ls_1MBS_1SCT.crd
Visualization: vmd -startup ls_1MBS_1SCT.vmd
Global Search: Niter=   1521
Local Search:  TIter=    313     AvIter=   31     MaxFound=   9     MaxNoRep=   9

C(AB000)=      0.453       d(AB000)=     84.844
C(AB001)=      0.365       d(AB001)=     91.410
C(AB002)=      0.352       d(AB002)=     92.346
C(AB003)=      0.347       d(AB003)=     92.635
C(AB004)=      0.347       d(AB004)=     92.677
C(AB005)=      0.344       d(AB005)=     92.857
C(AB006)=      0.341       d(AB006)=     93.088
C(AB007)=      0.340       d(AB007)=     93.169
C(AB008)=      0.312       d(AB008)=     95.097


---------------------------------------------------------------------------------
  END LSIM LOG FILE
--------------------------------------------------------------------------------- 

The output file prompts the similarity indices and molecular distances, while the aligned coordinates are stored in sets of ls_*.pdb files. Each file contains a single structure. In the example, ls_1MBS.pdb stores the 1MBS coordinates at the LSim standard orientation, and ls_1MBS_1SCT.pdb stores the 1SCT coordinates aligned with respect ls_1MBS. Multiple, local alignments are stored as trajectory files ls_*.crd.

For convenience, a VMD script is also generated. Visualization of a single or multiple, local alignments is feasible by typing the command:

vmd -startup ls_1MBS_1SCT.vmd

Download

LSim v 1.0.0

License

Pere Constans, Copyright 2001-2004. All rights reserved.

This Software is provided free of charge and in the hope that it will be a research and teaching tool for the analysis and evaluation of molecular similarity. The Software is intellectual property owned by the author, and all rights, title and interest, including copyright, remain with the author. The author grants, and Licensee hereby accepts, a license to use the Software for personal, academic or non-profit research purposes only. The user agrees that any reports or published results obtained with the Software will acknowledge its use by the appropriate citation as follows:

“Constans, P. Linear Scaling Approaches to Quantum Macromolecular Similarity: Evaluating the Similarity Function. J. Comput. Chem. 23, 1305-1313, 2002.”

Electronic documents will include a direct link to the LSim home page at https://www.molspaces.com/lsim/

NO WARRANTY

THIS SOFTWARE IS PROVIDED “AS IS” AND THE AUTHOR MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK, OR OTHER RIGHTS. LICENSEE ASSUMES THE ENTIRE RISK AS TO THE RESULTS AND PERFORMANCE OF THE SOFTWARE AND/OR ASSOCIATED MATERIALS. LICENSEE AGREES THAT THE AUTHOR SHALL NOT BE HELD LIABLE FOR ANY DIRECT,INDIRECT, CONSEQUENTIAL, OR INCIDENTAL DAMAGES WITH RESPECT TO ANY CLAIM BY LICENSEE OR ANY THIRD PARTY ON ACCOUNT OF OR ARISING FROM THIS AGREEMENT OR USE OF THE SOFTWARE AND/OR ASSOCIATED MATERIALS.

UNDERSTOOD AND AGREED.

Installation

Unpack the distribution file:

tar -xzvf lsim-linux.tar.gz

Move to file directory:

cd lsim.1.0.0\

Copy, move or link the executable file lsim to an appropriate location -and make sure lsim is accessible through the PATH environment variable-, e.g.:

cp lsim /usr/bin

Set variable LSIMDIR to point to the chosen LSim directory, e.g.:

setenv LSIMDIR /home/olaguer/progs/lsim.1.0.0


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