COACH protocols

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COACH specifications

Information


Unique identifier OMICS_03795
Name COACH
Alternative names COnsensus ApproaCH, COACH-D
Interface Web user interface
Restrictions to use None
Input data A structure or a sequence.
Input format PDB, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang <>

Publications for COnsensus ApproaCH

COACH in pipeline

2017
PMCID: 5569632
PMID: 28856159
DOI: 10.1155/2017/4658584

[…] the compatibility of the model with its amino acid sequence, to verify the geometrical and stereochemical constraints of the model and to determine the overall quality factor respectively. the coach server (https://zhanglab.ccmb.med.umich.edu/coach) [, ] was used to identify the binding domain of the above generated exni model., the 3d structure of the oligoxylose ligand was constructed […]


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COACH in publications

 (20)
PMCID: 5898002
PMID: 29650021
DOI: 10.1186/s12934-018-0908-9

[…] []. the c-score for the vioa model is 1.15, indicating a high degree of structural homology to the templates, which is additionally confirmed by the low rmsd of 4.1 ± 2.8 å. coach was then used for protein–ligand-binding site prediction [, ]., the cytotoxicity of compounds was measured by the mtt (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide; […]

PMCID: 5897026
PMID: 29649335
DOI: 10.1371/journal.pone.0195783

[…] server []. modelled protein structure was refined using modrefiner []. calcium ions binding sites were predicted using raptor x binding online server (http://raptorx.uchicago.edu/bindingsite/) or coach for protein-ligand binding site prediction (http://zhanglab.ccmb.med.umich.edu/coach/) []. various domains of lslpr protein was predicted using smart (http://smart.embl-heidelberg.de/) []. […]

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

[…] to verify their posterior probabilities of fold family classification., quality of the predicted structure was analyzed using structural validation algorithms prosa () and rampage ()., the coach (; ) (http://zhanglab.ccmb.med.umich.edu/coach/) bundled tm-site based on existing benchmarked studies was used to compare the structure of a sub-sequence from the first to last binding […]

PMCID: 5697364
PMID: 29157307
DOI: 10.1186/s13071-017-2523-8

[…] a ramachandran plot [] and errat []., structural conservation was calculated and visualized using endscript/espript v. 3.0 [] with the pdbaa95 database, e-value of 1e-12, and contact range of 2.7 å. coach [] was used to predict ligand-binding sites in csmrp4. sdf files for bile acids were retrieved from the pubchem database [] as of august 2017 and transformed into the mol2 format using […]

PMCID: 5611760
PMID: 28979293
DOI: 10.3389/fgene.2017.00125

[…] was submitted to the program modrefiner (), which refined all the stems giving a better resolution for each ancestral model. after refinement, each structural model was submitted to the program coach () to infer which molecule best binds to the binding site of the ancestral proteins. in all programs, the default parameters were used., for the comparative analysis between the ancestral […]


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COACH institution(s)
Department of Computational Medicine and Bioinformatics and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
COACH funding source(s)
Supported in part by the NSF Career Award (DBI 0746198) and the National Institute of General Medical Sciences (GM083107, GM084222).

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