3-D Structural Features

This section includes tools for searching for structural motifs, biochemical features found in protein structures, and functional sub-structures such as binding sites.

Found 125 links

Displaying 125 links

TitleTypeCitation CountURL
3D-partner
27
http://3d-partner.life.nctu.edu.tw/
3DEM Loupe
N/A
http://3demloupe.cnb.csic.es
3DLigandSite
21
http://www.sbg.bio.ic.ac.uk/3dligandsite
3dLOGO
98
http://3dlogo.uniroma2.it/3dLOGO/home.html
3DTF
N/A
http://cogangs.biobase.de/3dtf/
3V
11
http://3vee.molmovdb.org
Adepth
N/A
http://biodev.cea.fr/adepth
ALADYN
6
http://aladyn.escience-lab.org
AnalyCys
N/A
http://bioinformatics.univ-reunion.fr/analycys/
ANCHOR
12
http://structure.pitt.edu/anchor
Andrej Sali Lab
627
http://salilab.org/our_resources.shtml
ArchPred
26
http://manaslu.aecom.yu.edu/loopred/
BhairPred
45
http://www.imtech.res.in/raghava/bhairpred/
BioInfo3D
24
http://bioinfo3d.cs.tau.ac.il/
BioMe
N/A
http://metals.zesoi.fer.hr
BSDD
1
http://iris.physics.iisc.ernet.in/bsdd/
CAPS-DB
0
http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home
CASTp
1616
http://sts.bioengr.uic.edu/castp/
Catalytic Site Identification
N/A
http://mvirdb.llnl.gov/css
CCRXP
3
http://ccrxp.netasa.org
CHC_FIND
4
http://schubert.bio.uniroma1.it/CHC_FIND/index.html
CisRegTest
9
http://www.moseslab.csb.utoronto.ca/alan/cis_reg_test.html
CMWeb
N/A
http://cmweb.enzim.hu
COFACTOR
N/A
http://zhanglab.ccmb.med.umich.edu/COFACTOR
COLORADO-3D
50
http://asia.genesilico.pl/colorado3d/
ConSeq
181
http://conseq.bioinfo.tau.ac.il/
ConSurf
1112
http://consurf.tau.ac.il/
Cpred
N/A
http://sarst.life.nthu.edu.tw/CPred
CSpritz
3
http://protein.bio.unipd.it/cspritz/
DBCP
7
http://120.107.8.16/dbcp
DR.Bind
N/A
http://dnasite.limlab.ibms.sinica.edu.tw
eF-seek
409
http://ef-site.hgc.jp/eF-seek/index.jsp
ET Report Maker
36
http://mammoth.bcm.tmc.edu/report_maker/
EVAcon
15
http://www.pdg.cnb.uam.es/eva/con/index.html
FeatureMap3D
11
http://www.cbs.dtu.dk/services/FeatureMap3D/
FF - Fragment Finder
8
http://cluster.physics.iisc.ernet.in/ff/
FoldMiner and LOCK 2
28
http://foldminer.stanford.edu/
Fpocket
15
http://bioserv.rpbs.univ-paris-diderot.fr/fpocket
Gene3D
3
http://gene3d.biochem.ucl.ac.uk/WebServices/
GlobPlot
481
http://globplot.embl.de/
Glyprot
62
http://www.glycosciences.de/modeling/glyprot/php/main.php
H++
215
http://biophysics.cs.vt.edu/H++
Harmony
13
http://caps.ncbs.res.in/harmony/
I2I-SiteEngine
62
http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/
ICGEBnet Protein Tools
191
http://www.icgeb.org/protein/
iMOT
10
http://caps.ncbs.res.in/imot/iMOTserver.html
IntFOLD
9
http://www.reading.ac.uk/bioinf/IntFOLD/
KFC Server
29
http://www.mitchell-lab.org/kfc
KINARI-Web
8
http://kinari.cs.umass.edu/
KinDOCK
11
http://abcis.cbs.cnrs.fr/kindock/
KNOTS
127
http://knots.mit.edu/
MAPPIS
43
http://bioinfo3d.cs.tau.ac.il/MAPPIS
MCPep
N/A
http://bental.tau.ac.il/MCPep/
MolAxis
13
http://bioinfo3d.cs.tau.ac.il/MolAxis
MOLEonline 2.0
N/A
http://mole.upol.cz/
MolLoc
10
http://bcb.dei.unipd.it/MolLoc
MolSurfer
50
http://projects.villa-bosch.de/dbase/molsurfer/
MPlot
2
http://proteinformatics.charite.de/mplot/
MultiBind
43
http://bioinfo3d.cs.tau.ac.il/MultiBind
NNcon
28
http://casp.rnet.missouri.edu/nncon.html
NRSAS
2
http://www.receptors.org/NR/servers/html/
Nucleos
N/A
http://nucleos.bio.uniroma2.it/nucleos/
OPM database
2
http://opm.phar.umich.edu/
Paratome
N/A
http://www.ofranlab.org/paratome/
PAST
16
http://past.in.tum.de/
PBSword
N/A
http://pbs.rnet.missouri.edu
PCFamily
3
http://pcfamily.life.nctu.edu.tw
PDB2PQR Server
581
http://pdb2pqr.sourceforge.net/
pdbFun
32
http://pdbfun.uniroma2.it/
PDBSiteScan
63
http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html
PDB_Hydro
27
http://lorentz.immstr.pasteur.fr/solvate_mutate.php
PFP
127
http://pfp.technion.ac.il/
PHEMTO
8
http://phemto.orgchm.bas.bg/
PHEPS
13
http://pheps.orgchm.bas.bg/home.html
Phosfinder
1
http://phosfinder.bio.uniroma2.it
PI2PE
473
http://pipe.scs.fsu.edu/
PIC
88
http://crick.mbu.iisc.ernet.in/~PIC/
PINTS
277
http://www.russell.embl.de/pints/
pKD Server
178
http://enzyme.ucd.ie/cgi-bin/pKD/server_start.cgi
pKNOT-v2
17
http://pknot.life.nctu.edu.tw/
PocketQuery
N/A
http://pocketquery.csb.pitt.edu
POLYVIEW-MM
52
http://polyview.cchmc.org/conform.html
POPS
114
http://mathbio.nimr.mrc.ac.uk/wiki/POPS
PreBI
77
http://pre-s.protein.osaka-u.ac.jp/prebi/
PREDITOR
76
http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py
ProBiS
18
http://probis.cmm.ki.si
PROFEAT
84
http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi
ProFunc
267
http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/
ProKware
1
http://ProKware.mbc.nctu.edu.tw/
ProMateus
251
http://bioportal.weizmann.ac.il/promate/
ProSAT2
26
http://projects.villa-bosch.de/dbase/ps2/
ProSMoS
6
http://prodata.swmed.edu/ProSMoS/
ProtChemSI
1
http://pcidb.russelllab.org/
Protein Dipole Server
38
http://bioportal.weizmann.ac.il/dipol/
Protein Frustratometer
N/A
http://lfp.qb.fcen.uba.ar/embnet/charge.php?app=Frustratometer&chains=NO
Protein Peeling 3 D
26
http://www.dsimb.inserm.fr/dsimb_tools/peeling3/
Protemot
16
http://protemot.csbb.ntu.edu.tw/
PSCDB
1
http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/
RASMOT-3D PRO
5
http://biodev.extra.cea.fr/rasmot3d/
RCI
48
http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.py
ReadOut
318
http://gibk26.bio.kyutech.ac.jp/jouhou/readout/
RHYTHM
5
http://proteinformatics.charite.de/rhythm/
RNAcontext
9
http://www.cs.toronto.edu/~hilal/rnacontext/
RNSC
275
http://www.cs.utoronto.ca/~juris/data/rnsc/
SBSPKS
14
http://www.nii.ac.in/sbspks.html
SCit
16
http://bioserv.rpbs.jussieu.fr/cgi-bin/SCit
SCRATCH
295
http://www.igb.uci.edu/servers/psss.html
SDM
7
http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php
seeMotif
2
http://seemotif.csie.ntu.edu.tw
SiteEngine
51
http://bioinfo3d.cs.tau.ac.il/SiteEngine/
SITEHOUND-web
21
http://sitehound.sanchezlab.org
SLITHER
5
http://bioinfo.mc.ntu.edu.tw/slither/
SMAP-WS
10
http://kryptonite.ucsd.edu/opal2/GetServicesList.do
SPACER
N/A
http://allostery.bii.a-star.edu.sg/
SplitPocket
10
http://pocket.uchicago.edu/
SPRITE
N/A
http://mfrlab.org/grafss/sprite
Sride
67
http://sride.enzim.hu/
STING Millenium
168
http://luna.bioc.columbia.edu/SMS/STINGm/
StSNP
18
http://ilyinlab.org/StSNP/
SuperLooper
20
http://bioinf-applied.charite.de/superlooper/
SWAKK
16
http://oxytricha.princeton.edu/SWAKK/
TopMatch
62
http://topmatch.services.came.sbg.ac.at/
Vienna-PTM
N/A
http://vienna-ptm.univie.ac.at
VLDP
N/A
http://www.dsimb.inserm.fr/dsimb_tools/vldp
WebFEATURE
121
http://feature.stanford.edu/webfeature/

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