Protein-nucleic acid interactions predicting bioinformatics portal

Protein-DNA/RNA Interaction Database Resources

Type Name Working status URLs
Structure Databases BIPA - http://www-cryst.bioc.cam.ac.uk/bipa
PDIdb 2.0 Yes http://melolab.org/pdidb
3D-footprint Yes http://floresta.eead.csic.es/3dfootprint
ProNIT 2.0 - http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
NPIDB - http://npidb.belozersky.msu.ru/
PRIDB Yes http://bindr.gdcb.iastate.edu/PRIDB
ProNet DB Yes https://proj.cse.cuhk.edu.hk/aihlab/pronet/
PDBsum Yes http://www.ebi.ac.uk/thornton-srv/databases/pdbsum
PNIDB - http://server.malab.cn/PNIDB/index.html
PNATDB Yes http://chemyang.ccnu.edu.cn/ccb/database/PNAT/index.php/home/index
PDBbind+ Yes http://pdbbind-plus.org.cn/
Function Databases DPInteract Yes http://arep.med.harvard.edu/dpinteract
EcRBPome Yes http://caps.ncbs.res.in/ecrbpome/
hPDI Yes http://bioinfo.wilmer.jhu.edu/PDI/
PRALINE Yes https://praline.tartaglialab.com/
RBPDB Yes http://rbpdb.ccbr.utoronto.ca/
DoRiNA2.0 Yes http://dorina.mdc-berlin.de
ProNAB Yes https://web.iitm.ac.in/bioinfo2/pronab/
RNAct Yes https://rnact.crg.eu/
CLIPdb - http://lulab.life.tsinghua.edu.cn/clipdb/
ATtRACT Yes http:// attract.cnic.es
ENPD Yes http://qinlab.sls.cuhk.edu.hk/ENPD/
oRNAment Yes https://rnabiology.ircm.qc.ca/oRNAment
EuRBPDB Yes http://EuRBPDB.syshospital.org
POSTAR3 - http://postar.ncrnalab.org
DNAproDB Yes https://dnaprodb.usc.edu/
IntAct Yes https://www.ebi.ac.uk/intact

Computational tools for predicting protein-nucleic acids interactions binding residues and binding sites

Type Name Working status URLs
Sequence DP-Bind Yes http://lcg.rit.albany.edu/dp-bind/
NewDNA-Prot - http://sourceforge.net/projects/newdnaprot/
PNImodeler Yes http://bclab.inha.ac.kr/pnimodeler
DRNApred Yes http://biomine.cs.vcu.edu/servers/DRNApred/
PRIdictor Yes http://bclab.inha.ac.kr/pridictor/
RNApred Yes http://www.imtech.res.in/raghava/rnapred/
NucBind Yes http://yanglab.nankai.edu.cn/NucBind
funDNApred Yes http://biomine.cs.vcu.edu/servers/funDNApred/
ProNA2020 Yes https://github.com/Rostlab/ProNA2020.git
DisoRDPbind Yes http://biomine.cs.vcu.edu/servers/DisoRDPbind/
NCBRPred Yes http://bliulab.net/NCBRPred/
DNAgenie Yes http://biomine.cs.vcu.edu/servers/DNAgenie/
RBPsuite Yes http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/
DeepTFactor Yes https://bitbucket.org/kaistsystemsbiology/deeptfactor
RNAProt Yes https://github.com/BackofenLab/RNAProt
PPRInt2 Yes https://webs.iiitd.edu.in/raghava/pprint2/
iDRNA-ITF Yes http://bliulab.net/iDRNA-ITF
DBpred Yes https://webs.iiitd.edu.in/raghava/dbpred
DeepDISOBind Yes https://www.csuligroup.com/DeepDISOBind/
ESM-NBR Yes https://github.com/pengsl-lab/ESM-NBR
CLAPE Yes https://github.com/YAndrewL/clape
MucLiPred Yes https://github.com/sethzhangjs/MucLiPred
Seq-RBPPred Yes http://rnabinding.com/RBPPred.html
Structure Multi-VORFFIP Yes http://www.bioinsilico.org/MVORFFIP
iDNAProt-ES Yes http://brl.uiu.ac.bd/iDNAProt-ES/
RPI-bind Yes http://ctsb.is.wfubmc.edu/publications/RPI-Bind-Pred.php
inpPDH Yes http://bioinfo.ahu.edu.cn/inpPDH
SNB-PSSM Yes https://github.com/ChunhuaLiLab/SNB_PSSM
PST-PRNA Yes http://www.zpliulab.cn/PSTPRNA
GraphBind Yes http://www.csbio.sjtu.edu.cn/bioinf/GraphBind
GraphSite Yes https://biomed.nscc-gz.cn/apps/GraphSite
NABind Yes http://liulab.hzau.edu.cn/NABind/
PNAbind Yes https://github.com/jaredsagendorf/pnabind
EquiPNAS Yes https://github.com/Bhattacharya-Lab/EquiPNAS
Sequence/Structure RNAProSite Yes http://lilab.ecust.edu.cn/NABind
iDeepS Yes https://github.com/xypan1232/iDeepS
NucleicNet Yes http://www.cbrc.kaust.edu.sa/NucleicNet/
DNABind Yes http://mleg.cse.sc.edu/DNABind/

Computational tools for predicting protein-nucleic acids interactions binding conformations

Type Name Working status URLs
Rigid Docking FTDock/3D-Dock - http://www.sbg.bio.ic.ac.uk/docking/ftdock.html
HexServer - http://hexserver.loria.fr/
ZDOCK Yes https://zdock.umassmed.edu/
PyDockweb Yes https://life.bsc.es/pid/pydockweb
DOT 2.0 Yes https://www.sdsc.edu/CCMS/DOT/
PEPSI-Dock Yes https://team.inria.fr/nano-d/software/PEPSI-Dock
3dRPC/RPDock Yes http://biophy.hust.edu.cn/new/3dRPC
GRAMM Yes https://gramm.compbio.ku.edu/
P3DOCK Yes http://www.rnabinding.com/P3DOCK/P3DOCK.html
pyDockDNA Yes https://model3dbio.csic.es/pydockdna
PatchDock Yes http://bioinfo3d.cs.tau.ac.il
NPDock Yes http://genesilico.pl/NPDock
FroDock - http://sbg.cib.csic.es/Software/FRODOCK/
Semi-Flexible Docking PIPER Yes https://www.schrodinger.com/products/piper
ClusPro Yes https://cluspro.org/
RosettaDock Yes https://antibody.graylab.jhu.edu/
PyRy3D Yes https://genesilico.pl/pyry3d/
ICM-DISCO Yes -
HADDOCK Yes https://wenmr.science.uu.nl/haddock2.4/
ParaDock Yes http://bioinfo3d.cs.tau.ac.il/ParaDock/
ClustENMD Yes https://github.com/prody/ProDy
Flexible Docking MPRDock Yes http://huanglab.phys.hust.edu.cn/mprdock/
HDOCK Yes http://hdock.phys.hust.edu.cn/
SwarmDock - http://bmm.cancerresearchuk.org/%7ESwarmDock/
iATTRACT Yes -
ATTRACT Yes -
PRIME 2.0.1 Yes http://www.rnabinding.com/PRIME2.0.1/PRIME2.0.1.html
LightDock Yes https://server.lightdock.org/job/quick/step/1
ModelX Yes http://modelx.crg.eu
RoseTTAFoldNA Yes https://github.com/uw-ipd/RoseTTAFold2NA

State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural

Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University,

Guiyang, China

E-mail: gefei_hao@foxmail.com

Top