TM-fold statistics

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TM-fold specifications

Information


Unique identifier OMICS_16804
Name TM-fold
Interface Web user interface
Restrictions to use None
Input data Two protein structures.
Input format .PDB
Output data The probability for the structures belonging to the same SCOP/CATH Fold family.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Yang Zhang <>

Information


Unique identifier OMICS_16804
Name TM-fold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two protein structures.
Input format .PDB
Output data The probability for the structures belonging to the same SCOP/CATH Fold family.
Computer skills Advanced
Stability Stable
Source code URL https://zhanglab.ccmb.med.umich.edu/TM-fold/TMfold.tar.gz
Maintained Yes

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Documentation


Maintainer


  • person_outline Yang Zhang <>

Publication for TM-fold

TM-fold in publications

 (4)
PMCID: 5768738
PMID: 29335499
DOI: 10.1038/s41467-017-02741-4

[…] from the lateral side of tms., sequence homology search combined with phylogenetic analyses enabled us to reveal some unique features of abc3 family transporters, which usually possess an 8-tm fold, and an insertion between tm1 and tm2 (fig. ). in addition, these transporters are most likely combined with one or two partners to accomplish various functions. in many cases, these unique […]

PMCID: 5825884
PMID: 29492339
DOI: 10.7717/peerj.4396

[…] homologs. iterative threading assembly refinement (i-tasser) was used to model the three-dimensional structure of pb263r. the posterior probability of fold family assignment was calculated using tm-fold, and biological function was assigned using tm-site, raptorxbinding, gene ontology, and tm-align. our results suggests that pb263r has the features of a tata-binding protein and is thus […]

PMCID: 5145181
PMID: 27930690
DOI: 10.1371/journal.pone.0167718

[…] crystal structure of hgcgr [] (pdb file 4l6r)., sequence alignments show that almost all of the amino acids identified in the 7tm crystal structures of hgcgr engaged in stabilizing the receptor's tm fold and in the interactions between different pairs of transmembrane helices are conserved in the corresponding positions in the transmembrane domains of zfgpcr and hglp-1rs () [] (pdb file […]

PMCID: 4837479
PMID: 27088252
DOI: 10.1038/ncomms11336

[…] anomalous scattering and refined at a resolution of 3.7 å to an r-factor of 29.6% and rfree of 32.7% ()., the overall structure of uapa contains 14 transmembrane domains (tms) organized into a 7+7 tm fold divided into a core (tms 1–4 and 8–11) and a gate (tms 5–7 and 12–14) domain, similar to uraa ( and ). a key feature is that tms 3 and 10 only extend halfway through the protein, […]


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TM-fold institution(s)
Department of Medical School, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Molecular Biosciences, Center for Bioinformatics, University of Kansas, Lawrence, KS, USA
TM-fold funding source(s)
This work was supported by the Alfred P. Sloan Foundation NSF Career Award (DBI 0746198), and the National Institute of General Medical Sciences (GM083107, GM084222).

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