4. Crystallographic programs and other resources relevant for
RNA–protein crystallography (all accessed in March 2021):
CCP4 SUITE. A collection of programs covering most computational aspects of macromolecular crystallography, which
is freely available for academic use and can be downloaded
from http://www.ccp4.ac.uk/.
COOT. A macromolecular model building, model completion,
and validation program, particularly suitable for protein
modeling using X-ray data. COOT is widely used in the
crystallographic community for manual and automated
model building and is freely available for academic and
industrial users from https://www2.mrc-lmb.cam.ac.uk/
personal/pemsley/coot/ (Linux distribution) or http://
bernhardcl.github.io/coot/wincoot-download.html
(WINCOOT, Windows version). WINCOOT can also be
installed as an optional component with the CCP4 software suite. Extensive documentation is available on the
COOT
Wiki
page
(https://strucbio.biologie.unikonstanz.de/ccp4wiki/index.php/Coot).
IDEEPE predicts RNA–protein binding sites from RNA
sequences by combining global and local CNNs and identifies experimentally verified binding motifs (https://
github.com/xypan1232/iDeepE).
I-TASSER. A web-based or stand-alone software package for
protein structure and function modeling (https://
zhanglab.ccmb.med.umich.edu/I-TASSER/).
MOLPROBITY. A structure-validation web service that provides evaluation of model quality at both the global and
local levels for both proteins and nucleic acids (http://
molprobity.biochem.duke.edu).
MOSFLM. A program for integrating crystal diffraction data.
Linux, Mac, and Windows distributions are freely available
to academic and industrial users (https://www.mrc-lmb.
cam.ac.uk/harry/imosflm/ver722/introduction.html).
NPDOCK. A web server for modeling RNA–protein and
DNA–protein complex structures (http://genesilico.pl/
NPDock).
PROTEIN DATABASE (PDB). Archive of experimentally
determined structures (https://www.rcsb.org/).
PHASER. A program for phasing macromolecular crystal
structures with maximum likelihood methods, which is
available through the PHENIX and CCP4 software suites.
PHENIX. A software suite for the automated determination of
molecular structures using X-ray crystallography and other
methods (https://www.phenix-online.org/).
Studying RNA–Protein Complexes Using X-Ray Crystallography
443
RNA–protein crystallography (all accessed in March 2021):
CCP4 SUITE. A collection of programs covering most computational aspects of macromolecular crystallography, which
is freely available for academic use and can be downloaded
from http://www.ccp4.ac.uk/.
COOT. A macromolecular model building, model completion,
and validation program, particularly suitable for protein
modeling using X-ray data. COOT is widely used in the
crystallographic community for manual and automated
model building and is freely available for academic and
industrial users from https://www2.mrc-lmb.cam.ac.uk/
personal/pemsley/coot/ (Linux distribution) or http://
bernhardcl.github.io/coot/wincoot-download.html
(WINCOOT, Windows version). WINCOOT can also be
installed as an optional component with the CCP4 software suite. Extensive documentation is available on the
COOT
Wiki
page
(https://strucbio.biologie.unikonstanz.de/ccp4wiki/index.php/Coot).
IDEEPE predicts RNA–protein binding sites from RNA
sequences by combining global and local CNNs and identifies experimentally verified binding motifs (https://
github.com/xypan1232/iDeepE).
I-TASSER. A web-based or stand-alone software package for
protein structure and function modeling (https://
zhanglab.ccmb.med.umich.edu/I-TASSER/).
MOLPROBITY. A structure-validation web service that provides evaluation of model quality at both the global and
local levels for both proteins and nucleic acids (http://
molprobity.biochem.duke.edu).
MOSFLM. A program for integrating crystal diffraction data.
Linux, Mac, and Windows distributions are freely available
to academic and industrial users (https://www.mrc-lmb.
cam.ac.uk/harry/imosflm/ver722/introduction.html).
NPDOCK. A web server for modeling RNA–protein and
DNA–protein complex structures (http://genesilico.pl/
NPDock).
PROTEIN DATABASE (PDB). Archive of experimentally
determined structures (https://www.rcsb.org/).
PHASER. A program for phasing macromolecular crystal
structures with maximum likelihood methods, which is
available through the PHENIX and CCP4 software suites.
PHENIX. A software suite for the automated determination of
molecular structures using X-ray crystallography and other
methods (https://www.phenix-online.org/).
Studying RNA–Protein Complexes Using X-Ray Crystallography
443