LaJolla

LaJolla is an algorithm that can superimpose protein and RNA structures.

It's peer reviews and published in Algorithms 2009:

Bauer, R.A.; Rother, K.; Moor, P.; Reinert, K.; Steinke, T.; Bujnicki, J.M.; Preissner, R.
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2009, 2, 692-709. http://www.mdpi.com/1999-4893/2/2/692

Usage

Prerequisities

In order to use LaJolla you need first of all JDK 1.7 upwards. You can then get LaJolla here: https://github.com/raphaelbauer/lajolla/releases/latest

Simply download the file "lajolla.jar" and store it.

Lajolla can operate in 3 different modes. One for superimposing protein structures and two for superimposing RNA structures.

Superimposing proteins

usage: java -cp lajolla.jar PRO [options]

-am,--allmodels                   Deal with all models (slower) (DEFAULT:
                                  false)
-h,--help                         Print help for this application
-nr,--numres <arg>                Number of results to write out per
                                  target found: 1)
-o,--outputdir <arg>              Directory where to store result files
-q,--query <arg>                  query pdb file (directory or file)
-ref,--minrefinementscore <arg>   minimum refinement score needed
                                  (DEFAULT: 0.2)
-sm                               Score based on smaller structure
                               (symmetric score)
-t,--target <arg>                 target pdb file (directory or file)
-zn,--ngramsize <arg>             ADVANCED: size of ngram window
                               (DEFAULT: 18)

Superimposing RNA structures (based on eta theta angles)

usage: java -cp lajolla.jar RNA [options]

-am,--allmodels                   Deal with all models (slower) (DEFAULT:
                                  false)
-h,--help                         Print help for this application
-nr,--numres <arg>                Number of results to write out per
                                  target found: 1)
-o,--outputdir <arg>              Directory where to store result files
-q,--query <arg>                  query pdb file (directory or file)
-ref,--minrefinementscore <arg>   minimum refinement score needed
                                  (DEFAULT: 0.2)
-sm                               Score based on smaller structure
                                  (symmetric score)
-t,--target <arg>                 target pdb file (directory or file)
-zn,--ngramsize <arg>             ADVANCED: size of ngram window
                                  (DEFAULT: 7)

Superimposing RNA structures (based "suite" angles)

usage: java -cp lajolla.jar RNASuite [options]

-h,--help                         Print help for this application
-o,--outputdir <arg>              Directory where to store result files
-q,--query <arg>                  query suite file
-ref,--minrefinementscore <arg>   minimum refinement score needed
                                  (DEFAULT: 0.3)
-t,--target <arg>                 target suite file
-zn,--ngramsize <arg>             ADVANCED: size of ngram window
                                  (DEFAULT: 7)