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Protocols

LOMETS specifications

Information


Unique identifier OMICS_10830
Name LOMETS
Alternative name Local Meta-Threading-Server
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Protein sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang

Publications for Local Meta-Threading-Server

LOMETS citations

 (115)
library_books

Characterization of a novel organic solute transporter homologue from Clonorchis sinensis

2018
PLoS Negl Trop Dis
PMCID: 5942847
PMID: 29702646
DOI: 10.1371/journal.pntd.0006459

[…] The top 10 3D models of CsOST-N and -C domains were built based on multiple templates using LOMETS [] and refined using YASARA energy minimization []. A final 3D model of each CsOST domain was determined according to stereochemical quality assessment as well as high structural similarity ind […]

library_books

Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

2018
Biotechnol Biofuels
PMCID: 5879799
PMID: 29619080
DOI: 10.1186/s13068-018-1084-1

[…] : TRIREDRAFT_69957) and submitted to the I-TASSER online server. The structure modeling approach used by this software is based on the sequence alignment to a protein template, which is identified by LOMETS, a method that selects the top ten alignments in a PDB library. The unaligned regions of the sequence are built through ab initio folding, by considering the lowest free energy states and minim […]

library_books

Genome Wide Identification of the Alba Gene Family in Plants and Stress Responsive Expression of the Rice Alba Genes

2018
Genes
PMCID: 5924525
PMID: 29597290
DOI: 10.3390/genes9040183

[…] selected the best template based on the QMEAN score value. The scores and the parameters of the selected templates for all OsAlba proteins are mentioned in .The amino acid sequences were submitted to LOMETS [] to generate 3D structures. The 3D structures predicted for OsAlba proteins () were aligned to their respective templates in the TM-align server []. The predicted model was further analyzed i […]

library_books

Identification and Characterization of C type Lectins in Ostrinia furnacalis (Lepidoptera: Pyralidae)

2018
PMCID: 5842395
DOI: 10.1093/jisesa/iey011

[…] nement (I-TASSER) server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) for the prediction of tertiary structure. The representative structural template was identified from PDB by a locally installed LOMETS meta-threading server. Models were constructed by iterative TASSER simulations. The generated PDB files were then visualized with Pymol Molecular Graphics System. […]

call_split

The Immunological Regulation Roles of Porcine β 1, 4 Galactosyltransferase V (B4GALT5) in PRRSV Infection

2018
PMCID: 5837993
PMID: 29546034
DOI: 10.3389/fcimb.2018.00048
call_split See protocol

[…] It was a hierarchical approach to forecast structures and functions of multiple proteins. It would recognize the structural template from the Protein Data Bank (PDB) through the multi-threaded method LOMETS, which built a full-length atomic model through iterative template fragment simulated atomic assembly. The 3D model was then threaded through the BioLiP for ligand-protein binding database to i […]

call_split

PhcrTx2, a New Crab Paralyzing Peptide Toxin from the Sea Anemone Phymanthus crucifer

2018
Toxins
PMCID: 5848173
PMID: 29414882
DOI: 10.3390/toxins10020072
call_split See protocol

[…] ng_simple1&userid= USERID&token=TOKEN []) with a template-free approach (i.e., Phyre2 v2.0 at http://www.sbg.bio.ic.ac.uk/phyre2 [], I-Tasser v5.0 at https://zhanglab.ccmb.med.umich.edu/I-TASSER/ [], LOMETS v4.0 at http://zhanglab.ccmb.med.umich.edu/LOMETS/ [], and RaptorXat http://raptorx.uchicago.edu/ []). The predicted 3D models of PhcrTx2 were subjected to a series of tests for evaluating thei […]

Citations

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LOMETS institution(s)
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS, USA
LOMETS funding source(s)
The project is partially supported by KU Start-up Fund 06194 and NFGRF 2302003.

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