SAM-T08 protocols

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SAM-T08 specifications

Information


Unique identifier OMICS_24293
Name SAM-T08
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Output data A 3D model.
Output format PDB
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline Kevin Karplus <>

Publication for SAM-T08

SAM-T08 in pipelines

 (6)
2016
PMCID: 4868595
PMID: 27190719
DOI: 10.7717/peerj.2023

[…] targetp 1.1 (http://www.cbs.dtu.dk/services/targetp/), netsurfp 1.1 (http://www.cbs.dtu.dk/services/netsurfp/), phyre2 (http://www.sbg.bio.ic.ac.uk/servers/phyre2/html/page.cgi?id=index), sam-t08 (http://compbio.soe.ucsc.edu/sam_t08/t08-query.html) and elm (http://elm.eu.org/search/)., the molecular test for the t. cf. atroviride biocontrol strain lu132 was developed based on pcr […]

2015
PMCID: 4493641
PMID: 26157619
DOI: 10.7717/peerj.1040

[…] ()., fadd homology models were generated using the swiss-model homology modeling server (; ; ) and the thermus thermophilus structure as the template, the i-tasser server (; ; ), and (iii) sam-t08 (; ; ; ; ; ; ; ). models were visualized in mac pymol (the pymol molecular graphics system, version 1.7rc1 schrödinger, llc.) and swiss-pdbviewer ()., fadd mutants generated by error prone […]

2015
PMCID: 4493641
PMID: 26157619
DOI: 10.7717/peerj.1040

[…] consistent measurements., fadd homology models generated using the swiss-model homology modeling server (; ; ) and the thermus thermophilus structure as the template, the i-tasser server (; ; ), and sam-t08 (; ; ; ; ; ; ; ), show that several of the fadd mutations cluster around a possible atp/amp entrance/exit channel ( and ). all models have features similar to those of known adenylating […]

2015
PMCID: 4714197
PMID: 26601946
DOI: 10.1074/jbc.M115.698589

[…] 2.0 () were undertaken using amino acids 175–519 of i-2 and amino acids 197–334 of os02g_25900 using both normal and intensive modeling modes. similar structural homology was also detected using the sam-t08, hmm-based protein structure prediction server (). side chain packing and energy minimization was performed using galaxyrefine (). the figures were generated using the pymol molecular […]

2012
PMCID: 3591116
PMID: 23484105
DOI: 10.1155/2013/294759

[…] fba, and atp a) showed the model length percentage more than 80%. while remaining four proteins (sps ii, sbe i, waxy, and prk) have less than 80% (). all 3d full length models were generated by sam-t08 (based on hmm) except sbe i. modeling of sbe i protein is done by i-tasser (using ab-intio approach) as shown in given figures (figures , , , , , , , , and ). , three-dimensional protein […]


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SAM-T08 in publications

 (24)
PMCID: 4771712
PMID: 26928467
DOI: 10.1371/journal.pone.0150153

[…] for fitting the curves can be obtained in the document–‘biomolecular binding kinetics assays on the octet platform’, downloaded from the website—http://www.fortebio.com/literature.html., hmm based sam-t08 [] online server (threading based structure prediction) was used to obtain the structure of c35. fasta format of the protein sequence is submitted for structure prediction. the model […]

PMCID: 4868595
PMID: 27190719
DOI: 10.7717/peerj.2023

[…] targetp 1.1 (http://www.cbs.dtu.dk/services/targetp/), netsurfp 1.1 (http://www.cbs.dtu.dk/services/netsurfp/), phyre2 (http://www.sbg.bio.ic.ac.uk/servers/phyre2/html/page.cgi?id=index), sam-t08 (http://compbio.soe.ucsc.edu/sam_t08/t08-query.html) and elm (http://elm.eu.org/search/)., the molecular test for the t. cf. atroviride biocontrol strain lu132 was developed based on pcr […]

PMCID: 4704623
PMID: 26691485
DOI: 10.1590/S1517-838246420140846

[…] also, for finding a rational template for misaligned parts of query sequence, sequence alignment and modeling (sam)-t08, a hmm-based protein prediction webserver (http://compbio.soe.ucsc.edu/sam_t08/t08-query.html) was used. in this method, first a cluster of hmm made by querying similar sequences and alignment was performed between a hmm database of structures and the constructed hmm […]

PMCID: 4619093
PMID: 26493560
DOI: 10.1186/s12859-015-0773-z

[…] positives [] and absolute values between 14 and 7 denote moderate similarity between query and hit []. the hhsearch scores are probabilities for match to be a true positive (true homolog). coma and sam_t08 report e-values as scores. descriptions of the scores are additionally provided in additional file . sequences of gmrs and gmrd domains of the gmrsd enzyme from e. coli ct596 (originally […]

PMCID: 4599002
PMID: 26306038
DOI: 10.1074/jbc.M115.672121

[…] recognition engine version 2.0 () were undertaken using amino acids 143–488 of rx1, using both normal and intensive modeling modes. similar structural homology was also detected using the sam-t08, hidden markov model-based protein structure prediction server (). all superpositions were performed using the ssm algorithm in coot (). models of rx1 based on cdc6/orc1 (pdb accession number […]


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SAM-T08 institution(s)
Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA, USA
SAM-T08 funding source(s)
Supported by National Institutes of Health (Grant 1 R01 GM068570- 01).

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