QRNAS: software tool for refinement of nucleic acid structures 

 

Program Summary: 

 

QRNAS is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues. 

 

Availability: 

 

QRNAS is free (GNU GPLv3+ license). The software is written in C++. Source code is available for GNU/Linux distributions.

For the compilation of QRNAS, a C++ compiler, such as GNU g++ is required. A Makefile is provided for the compilation of the package. Download the software from http://genesilico.pl/qrnas/ or clone it from https://github.com/sunandanmukherjee/QRNAS.git. Unzip the archive, and compile it with the command make to create an executable version of QRNAS. To execute the program use the command …/path/to/QRNAS/QRNA –i input.pdb –o output.pdb where input.pdb is the file to be optimized and output.pdb is the optimized structure. For more advanced usage of QRNAS, users should consult the user manual and the README.txt file in the QRNAS package.

 

Download QRNAS from: 

 

http://genesilico.pl/QRNAS/QRNAS.tar.gz

 

Datasets available from:

 

 http://genesilico.pl/QRNAS/QRNAS_data.tar.gz

 

User manual: 

Functionality        

Installation        

2.1 Installation on Linux machines        

2.1.1. Installation of C++ compiler and make        

2.1.2 Extraction of QRNAS        

2.1.3 Compiling QRNAs in sequential mode        

2.1.4 Compiling QRNAS in parallel mode        

2.1.5 Setting up environment variables for QRNAS        

2.2 Installation on Windows 10 machines        

2.3 Installation on Mac OS        

QRNAS usage        

3.1. Running QRNAS without configuration file        

3.2. Running QRNAS with the configuration file        

Running QRNAS with restraints        

4.1. Secondary structural restraints        

4.1.1. Vienna (dot-bracket) format        

4.1.2. Explicit restraints on base-pairs        

4.2. Long range restraints        

4.3 Positional restraints        

 

 

 

  1. Functionality

QRNAS is a software tool for fine-grained refinement of nucleic acid structures, dedicated to improving the quality of models generated by low- to medium-resolution methods commonly used, e.g., for RNA three-dimensional (3D) structure modeling. QRNAS is capable of handling RNA, DNA or chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues. The force-field used by QRNAS is a modified version of AMBER adopted to represent 107 modified nucleotides currently known to be present in RNA.

 

 

  1. Installation

QRNAS supports both Linux and Mac operating systems. It can also be installed and used under MS Windows, only if MS Windows Subsystem for Linux (WSL) is enabled.

2.1 Installation on Linux machines

2.1.1. Installation of C++ compiler and make

The QRNAS program is written in C++ language using the STL libraries. On GNU/Linux machines it can be compiled using g++ compiler. The g++ compiler can be installed using the following command on a Ubuntu, Debian or their derivatives:

 

$ sudo apt update

$ sudo apt upgrade

sudo apt install build-essential

 

On Fedora/Red Hat or its derivatives, the installation can be performed using the following command:

 

        $ sudo dnf install make gcc-c++

 

For openSUSE or its derivatives use the following command:

 

$ zypper install make gcc-c++

 

For Arch Linux use the following command:

 

$ pacman -S base-devel

 

Once the compiler is installed QRNAS can be extracted and compiled as described in 2.1.2.

 

2.1.2 Extraction of QRNAS

 

The QRNAS source code is provided as a standard tar.gz archive file. The file can be downloaded from the url: http://genesilico.pl/QRNAS/QRNAS.tar.gz. After downloading, the file can be extracted using the following command:

$ tar -xvzf QRNAS.tar.gz

 

The above command will create a new directory named QRNAS and extract the source inside it.

 

2.1.3 Compiling QRNAs in sequential mode

 

Although the default behavior of make command is to compile QRNAS in sequential mode (in this mode, it can run using only one processor at a time), it is also possible to compile QRNAS in parallel mode (see section 2.1.4).

 

The QRNAS directory contains all source codes, data directory and other files necessary for compilation and running of QRNAS. After extracting the files as mentioned in 2.1.2 the QRNAS can be compiled by entering the directory and running make command. All the sources will be compiled automatically to generate the binary file QRNAS.

 

$ cd QRNAS

make

 

 

 

2.1.4 Compiling QRNAS in parallel mode

 

Calculations of electrostatic interactions in QRNAS are written with the POSIX thread (pthread) library support. This allows the program to  the compiled with parallel computing support, which make use of multiple processors at the same time. In order to use this feature, the QRNAS program needs to be compiled in a parallel mode. This can be done by using the Makefile by running the following command:

        

        $ make parallel

 

2.1.5 Setting up environment variables for QRNAS

 

The following environmental variables can be set up for running QRNAS from shell outside the installation directory. The following commands can be run to add the environment variables to user’s bashrc from the QRNAS source directory:

 

        $ echo export PATH='$PATH':$(pwd) >>~/.bashrc

        $ echo export QRNAS_FF_DIR=$(pwd)/forcefield >>~/.bashrc

 

For changes to take place in the current shell the bashrc file needs to be sourced again. However, this step is not needed if you are opening a new shell environment. 

 

        $ source ~/.bashrc

 

This step is optional. The QRNAS_FF_DIR environment variable can be exported to set path to forcefield directory. In the absence of QRNAS_FF_DIR environment variable, QRNAS expect forcefield directory (or a symbolic link to the forcefield directory) in the current working directory.

 

2.2 Installation on Windows 10 machines

In order to use QRNAS on Microsoft Windows 10, the first step is to enable Windows Subsystem for Linux (WSL). This can done by running the following command from PowerShell or Windows Command

 

$ Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

$ sudo apt update

$ sudo apt upgrade

 

After rebooting the system, open windows command prompt and type bash, Follow the on-screen instructions and wait for installation to complete.

The remaining steps for installation are same as described in section 2.1

 

2.3 Installation on Mac OS

The first step is to install Xcode from the Mac App store. After installing the xcode, open Mac terminal app type the following command to install the command line tools necessary for compiling QRNAS

 

$ xcode-select --install

 

A pop-up windows will open and continue the installation following the on-screen instructions. The remaining steps for compilation and setting environment variables are same as described in section 2.1

 

 

 

 

 

 

 

 

  1. QRNAS usage

3.1. Running QRNAS without configuration file

Upon successful installation, QRNAS optimization can be performed from the command-line using the default parameters:

$ QRNA -i <input_pdb_file>

Example:

QRNA -i 1l2x.pdb

It minimizes 1l2x.pdb and writes the minimized structure in pdb format in every 100 steps as 1l2x_out_XXX.pdb where XXX is the number of step (e.g. 1l2x_out_100.pdb for 100th step).

However user can define the name of the output file:

$ QRNA -i <input_pdb_file> -o <output_file>

Example:

$ QRNA -i 1l2x.pdb -o 1l2x_QRNAS.pdb

In this case, the minimized output will be written as 1l2x_QRNAS_XXX.pdb where XXX is the number of step (e.g. 1l2x_QRNAS_100.pdb for 100th step).

QRNAS, with default verbosity, prints the messages including the energy values in console and does not record them in any file. To store this information in a log file, the following command can be used:

$ QRNA -i <input_pdb_file> -o <output_file> 2>&1> filename.log

Example:

$ QRNA -i 1l2x.pdb -o 1l2x_QRNAS.pdb 2>&1> 1l2x_QRNAS.log

 

3.2. Running QRNAS with the configuration file

        QRNAS optimization can be run using customized parameters (altering the default values). The alternate parameters should be provided in a configuration file. An example configuration file should be as following:

 

 

# Sample config file for QRNA 0.2

# Just uncomment the lines you need.

 

#INPUTPDB   ./1l2x.pdb

#OUTPUTPDB  ./1l2x_refined.pdb

#WRITEFREQ  1000        # Frequency of writing outputpdb (each xxx steps); by default 100

#TRAJECTORY 1           #{0,1}-Each outputPDB is written to a separate file; by default OFF

 

#VERBOSE        2           # {0,1,2,3} - verbosity; by default 1

 

#NSTEPS         20000   # Maximal number of steps; by default 100000

#CUTOFF         12.0        # Cutoff for van der Waals [Ang]; by default 12

#USEBORN        1           # {0,1} - Born electrostatics, i.e. implicit solvent (off/on); by default OFF

#ELECTR         0           # {0,1} Electrostatics (off/on); by default ON

#VDW            0           # {0,1} Van der Waals interactions (off/on); by default ON

 

#HBONDS         0           # {0,1} Hydrogen bonds (off/on); by default ON

                        # They are necessary to auto-detect secondary structure.

 

#SSDETECT   0           # {0,1} - Detect base pairs automatically, by default ON

#SSCONSTR   0           # {0,1} - Impose constraints on base pairs (off/on); by default ON

 

#MAXSTEP        1e-8        # Max step size for golden section search; by default 1e-4

#MINSTEP        1e-10  # Min step size for golden section search; by default 1e-8

                        # (In most cases these parameters are not recommended

                        # to be altered)

 

#NUMTHREADS  2          # Number of threads (parallel builds only!); by default 4

                        # Takes no effect in sequential builds of QRNA.

                        # Only calculations of electrostatics are currently parallelized.

 

#BLOWGUARD  0           # Protection against explosion due to high stress; by default ON

                        # It slows the minimization!

 

#POSRESTRAINTS 1        # {0,1} - Positional restraints (off/on), read from occupancy and beta-factors;

                        # by default OFF

 

# Secondary structure can be specified in two ways.

# The deprecated and retarded way is via Vienna notation. It applies to the first chain only:

#SECSTRUCT   (((....)))

# The kosher and robust way is via pairwise restraints specified in a separate file:

#RESTRFILE file_with_restraints.txt

 

The aforementioned example can be used for the optimization by uncommenting (by removing the ‘#’) the listed parameters in the file:

 

Example:

INPUTPDB   1l2x.pdb

OUTPUTPDB  1l2x_refined.pdb

WRITEFREQ  1000    # Frequency of writing outputPDB (each xxx steps); by default 100

#TRAJECTORY 1      #{0,1}-Each outputPDB is written to a separate file; by default OFF

#VERBOSE        2           # {0,1,2,3} - verbosity; by default 1

 

 

In the above example, the configuration file specifies 1l2x.pdb as input file (equivalent to -i argument in command-line) and 1l2x_refined.pdb as output file (equivalent to -o argument in command-line). The argument WRITEFREQ 1000, indicates QRNAS to write optimized structures after 1000 steps (instead of 100 which is default). QRNAS will ignore the last two lines (TRAJECTORY and VERBOSE since they are commented).

 

QRNAS can be run with configuration files using -c flag:

$ QRNA -c <configuration_file>

Example:

$ QRNA -c config.txt

However, if -i and -o values are provided, QRNAS ignore INPUTPDB and OUTPUTPDB mentioned in configuration file.

         $ QRNA -i 1l2x.pdb -o 1l2x_QRNAS.pdb -c config.txt

 

  1. Running QRNAS with restraints

4.1. Secondary structural restraints

Secondary structure can be specified in two ways:

4.1.1. Vienna (dot-bracket) format

One of the ways to assign secondary-structure is via Vienna notation. It applies to the first chain only and can be mentioned in the configuration file.

 

Example:

SECSTRUCT   (((....)))

 

4.1.2. Explicit restraints on base-pairs

Watson-Crick (canonical) base-pairs can be restrained by specifying appropriate chain identifiers and residue numbers:

 

BASEPAIR   B/1   A/32  

BASEPAIR   B/2   A/31  

BASEPAIR   B/3   A/30  

 

Any non-canonical base-pair will be ignored by QRNAS.

 

4.2. Long range restraints

        QRNAS allows users to restraints a pair of atoms by a certain distance as following:

 

DISTANCE   A/3/C4'   B/4/C3'        3        4        50

DISTANCE   A/4/C2'   B/5/O3'        4        4        100

DISTANCE   A/5/C1'   B/6/H2'        5.5  3.5        100

 

Distance restraints are implemented as simple harmonic forces. The first column indicates the keyword “Distance”, second and third columns indicate the pair of atoms to be restrained. Fourth and fifth columns specify the minimum and maximum values of the distance, respectively. The spring length is considered as the average of the minimum and maximum (in Angstroms). The last column specifies the spring force constant.

 

In the above example:

DISTANCE   A/3/C4'   B/4/C3'        3        4        50

the pair of atoms (C4' from residue 3 in chain A  &  C3' from residue 4 in chain B) are bound by a spring of rest length of 3.5 Å and force constant of 50 kcal/mol/Å2.

In case of:

DISTANCE   A/4/C2'   B/5/O3'        4        4        100

the pair of atoms (C2' from residue 4 in chain A  &  O3' from residue 5 in chain B) are bound by a spring of rest length of 4 Å and force constant of 100 kcal/mol/Å2.

 

The restraints can be provided by mentioning the restraints in a file using -m flag in command-line:

 

$ QRNA -i <input_pdb_file> -m <restraints_file>

Example:

 

        $ QRNA -i 1l2x.pdb -m 1l2x_restraints.txt

 

Configuration file (with -c flag) can also be used along with the restraints file. Alternatively, restraints file can be specified in configuration file. However, QRNAS will override the restraint file mentioned in configuration file if another restraint file is specified with -m flag in the command-line.

 

4.3 Positional restraints

QRNAS is able to restrain the positions of specified atoms. The two possibilities are “freezing” and/or “pinning down” individual atoms. These restraints can be implemented by altering the occupancy and B-factor column in the input pdb file.

If the occupancy of an atom is set equal to 0.00, its position is fixed / frozen, which means that will not be changed during the optimization.

If the occupancy is set between 0.00 and 1.00 , the residue is “pinned down” to its original position, and the B-factor value is treated as a radius of unrestricted movement from the starting position.

If the occupancy is set equal to 1.00, then the movement of the atom is not restricted (unless it is specified by other restraints).

 

After modifying the occupancy and B-factor columns of the pdb file, -P along with -i flag should be used to run QRNAS optimization as follows:

QRNA -P -i <input_pdb_file>

Example:

        $ QRNA -P -i 1l2x_occu_modified.pdb

Here 1l2x_occu_modified.pdb is the input structure with altered occupancy and B-factor columns.

 
 

Bug reports: 

 

All feedback, including bug reports and suggestions for new options to be implemented, should be sent to iamb@genesilico.pl