●I-TASSER ●QUARK ●LOMETS ●COACH ●COFACTOR ●MetaGO ●MUSTER ●SEGMER ●FG-MD ●ModRefiner ●REMO ●SPRING ●COTH ●BSpred ●SVMSEQ ●ANGLOR ●BSP-SLIM ●SAXSTER ●ThreaDom ●ThreaDomEx ●EvoDesign ●GPCR-I-TASSER ●BindProf ●BindProfX ●ResQ ●IonCom ●STRUM

●TM-score ●TM-align ●MM-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●NeBcon ●WDL-RF ●ATPbind

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●TM-fold ●DECOYS ●POTENTIAL ●RW ●HPSF ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12

RNA-align standalone package

RNA-align is a free and open-source RNA and DNA structure alignment program written in C++ (Read more).
• Download RNA-align source code. You need g++ to compile RNA-align:
  $ g++ -O3 -ffast-math -o RNAalign RNAalign.cpp -static
  or
  $ make clean; make RNAalign
  The "-static" flag should be deleted on Mac, which does not support static build.
  
• Download pre-compiled executable for 64bit Linux. Nevetheless, it is recommended that you download the source code and compile it on your machine, which gives higher speed to run the program.

RNA-align benchmark datasets

• Download 6,571,496 RNA pairs for training d₀.
• Download 963 RNA structures from 87 Rfam families for assessing the statistical significance of TM-score_RNA.
• Download 687 randomly selected subset of RNA structures for benchmarking the alignment accuracy and speed in comparison with third-party program.

RNA secondary structure (SS) assignment and file format conversion

These programs are not required for RNA-align to work. They are provided to allow reproduction of SS assignment results reported in the RNA-align paper.

• Download pre-compiled executable for the subroutine of coarse-grain SS assignment used in RNA-align. The source code of this program is available as part of the RNA-align source code and can be separately compiled by
$ make pdb2ss

Assign SS for PDB file 'pdb.pdb' by

$ ./pdb2ss pdb.pdb

• Download source code for our reference implement of full-atomic SS assignment based on angles and distances of atoms involved in hydrogen bond formation in base pairs. Assign SS for PDB file 'pdb.pdb' by
$ python ./3Dto2D.py pdb.pdb

• Download source code for the subroutine used by RNA-align server to converting mmCIF/PDBx format into PDB format. Compile the program with:
$ make cif2pdb

Convert PDBx/mmCIF file 'pdb.cif' into PDB format by:
$ ./cif2pdb pdb.cif > pdb.pdb