RCD Linux64

  • Last update: 06 March 2017
  • File size: 22.81 MB
  • Version: 1.11
  • Downloaded: 89
  • Author: López-Blanco JR, Canosa-Valls AJ, Li Y, and Chacón P
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##############################################
#  --- RCD v1.11 (from release v1.06)   ---  #
#  --- Chacon's lab - March 11th, 2016  ---  #
##############################################

This is the last stable version of RCD (v1.11) but testing is very limited.


----------------------------------------------------------
RCD v1.11 (Random Coordinate Descent protein loop closure)
----------------------------------------------------------

We provide statically linked 64-bit LINUX executables generated with Intel
and GNU compilers to minimize library dependence problems. Dynamic linking
was used for MPI parallelized versions (both GNU and Intel).

This is not the complete protocol for ab initio loop prediction detailed in
the paper Lopez-Blanco et al. NAR 2016 (see the complete reference below).
Please, contact us if you want to test this protocol in your local machine.

> Programs provided
-------------------
rcd        v1.11 --> Protein loop closure program.

*All the programs show a basic help text using the --help option.

> Binaries releases
-------------------

Pre-compiled binaries are available in the corresponding bin/ directory. You
can choose the appropriate release for your system:

 [Program]        Compiler    Libraries              Linkage
 -----------------------------------------------------------
*<TOOL>           Intel icpc  -                       static
 <TOOL>_gcc       GNU gcc     -                       static
*<TOOL>_mpi       Intel icpc  OpenMPI                dynamic

* Intel compiled binaries are the fastest alternatives.
<TOOL> corresponds to the name of the program.


------------
REQUIREMENTS
------------

This software release has been only tested with 64-bit Intel "icpc"
(v. 13.0.1) and GNU "gcc" (4.6.3) compilers.

Statically linked executables are ready-to-use (nothing else required).

The following libraries may be required only to run the pre-compiled binaries
of the MPI release(s):

> For Intel release(s):
-----------------------

- Intel's C++ Compiler - Current tested icpc version 13.0.1 (gcc version
4.6.0 compatibility).

Please, download and install the Intel C++ Compiler:
  "Intel C++ Composer XE for Linux" (current tested version is 2013.1.117)

Intel C++ Compiler can be obtained for free from Intel's web site:
http://software.intel.com/en-us/articles/non-commercial-software-download/

- MPI parallelized programs also require a MPI library (current tested version
in OpenMPI v.1.10.2). These MPI programs and the OpenMPI library were compiled
with Intel "icpc" compiler version 13.0.1 (gcc version 4.6.0 compatibility).
 
> For GNU releases:
-------------------

- An OpenMPI version for GNU compilers is not provided. Please, contact us
if you need an MPI parallelized version compiled with GNU compilers.


----------------------
RCD v1.11 IMPROVEMENTS
----------------------

The main improvements with respect to the original RCD (v1.0) are:

1) Fast backbone angle sampling based on neighbor-dependent Ramachandran
probability distributions.

2) MPI-parallelization.

3) Fast distance-orientation dependent energy filter.


------------------
RCD v1.11 TUTORIAL
------------------

In the sub-directories rcd_seok8/ and rcd_seok12/ we have included the 8 and 12
residues long benchmarks (20 cases each) used in the RCD+ paper. To perform
the loop closure just copy and paste the following commands:

 Go to the test directory
  $ cd rcd_seok12
 
 And perform the loop closure
  $ ../bin/rcd seok12.txt -n 10000 -r -t 0.90 -x dunbrack.bin --loco loco.score --loco_best 1000 --bench -o mybasename

 The input file (seok12.txt) is a plain text input file. That uses the
following simple format, one loop per line:

  <PDB_file> [Start_index] [End_index] [Chain_ID] [Loop_sequence]

 For example:
 
  1a8dA.pdb    155  166  A DLPDKFNAYLAN
  1arbA.pdb    182  193  A WQPSGGVTEPGS
  [and so on...]

 The other options were those used in the recent RCD+ server paper:
 
   -n <int>,  --nloops <int>
      Number of loops sampled.

   -r,  --randomize
      Randomize bond lengths and valence angles (small perturbation).

   -t <float>,  --threshold <float>
      Threshold for neighbor-dependent Ramachandran filter. Using 0.90
     accounts for the 90% of probability. (default=0.98)
     
   -x <string>,  --pdf <string>
      Dunbrack's Probability Density Function.

   --loco <string>
      Introducing a ICOSA energy data file (loco.score) enables
     ICOSA energy calculations.

   --loco_best <int>
      Number of lowest ICOSA-energy loops that will be further stored
     and processed (<nloops). (disabled by default)

   -o <string>,  --name <string>
      Output directory basename. By default, current date will be used as
     basename (e.g. run__11_May_2016__13h_23_06).

   --bench
      Considers non-native workflow but just using native-coordinates for
     RMSD benchmarking. (default = disabled)

 Note that both dunbrack.bin and loco.score files are required to use the
 neighbor-dependant Ramachandran sampling and the ICOSA energy filtration,
 respectively. Please, copy or link them to your working directory.

 We strongly recommend to run RCD in parallel. To this end, use the mpirun
 command with the MPI version of RCD:
  $ mpirun -n 4 ../bin/rcd_mpi seok12.txt -n 10000 -r -t 0.90 -x dunbrack.bin --loco loco.score --loco_best 1000 --ben
ch -o mybasename

The complete 12-residues test (rcd_seok12) takes around 36 minutes (108 s/case)
using the Intel binary and the 4 cores of an old Intel(R) Core(TM) i7 CPU 950
at 3.07GHz. The sequential version takes around two hours (7-8 minutes/case)
in the same machine.

You can check the closed loops (*_closed.pdb file) with your favourite
molecular visualization program.

RCD outputs the following files by default:

  <loop_PDB_name>_closed.pdb --> All closed loop models produced by RCD at
  selected Coarse-Graining level (a single Multi-PDB file).

  results.txt --> RCD's summary results file (plain text).

  <loop_PDB_name>_dh/val/len.pdb --> Text files with dihedral (dh), valence
  angles (val), and bond lengths (len) of all closed loops.

  <loop_PDB_name>_rmsd.txt --> Text file with loop RMSD vs. native and ICOSA or
  Bumps energies.
 
  <loop_PDB_name>.log --> Log file with detailed run options data.
 
In case you need more help to use RCD, please, feel free to contact us!


----------
REFERENCES
----------

Please, cite our work if our tools become useful for your research.

> Improved RCD method
---------------------
Lopez-Blanco JR, Canosa-Valls AJ, Li Y, and Chacon P (2016). RCD+: Fast loop
modeling server. NAR (DOI: 10.1093/nar/gkw395).

> Original RCD method
---------------------
Chys P and Chacon P (2013). Random coordinate descent with spinor-matrices and
geometric filters for efficient loop closure. J. Chem. Theory Comput. 9:1821-1829.


-------
CONTACT
-------

Please, feel free to contact with us!
(Any suggestion or bug report is welcome)

Jose Ramon Lopez-Blanco (PhD)
jrlopez(at)iqfr.csic.es

Pablo Chacon (PhD.)
pablo(at)chaconlab.org


Structural Bioinformatics Group
IQFR-CSIC - Madrid (Spain)
(http://chaconlab.org)