FTMAP protocols

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FTMAP specifications

Information


Unique identifier OMICS_03869
Name FTMAP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FTMAP

FTMAP in pipeline

2016
PMCID: 4866707
PMID: 27175900
DOI: 10.1371/journal.pcbi.1004935

[…] of simulations performed are summarized in . the structural models and trajectory data are available as supporting data ( and data sets), mapping of interaction hotspots was performed using the ftmap algorithm (http://ftmap.bu.edu []). trajectory visualisation, secondary structure analysis (based on stride; [], imaging and file conversion was performed with vmd v.1.9.2 []. cpptraj […]


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FTMAP in publications

 (42)
PMCID: 5912754
PMID: 29684031
DOI: 10.1371/journal.pone.0195980

[…] with maxcluster [] using the rmsd distance between the data point represented by the allosteric binding site residues identified previously. potential binding pockets were identified using ftmap [] and a consensus binding site was built around the allosteric binding site residues in the tm domain., the charmm-gui was again used to build an md simulation system for the highest scoring […]

PMCID: 5913730
PMID: 29529862
DOI: 10.1021/acschembio.7b01093

[…] we embarked on a fragment screening campaign to explore the propensity of the protein surface to bind small molecules., first, we assessed the ligandability of the histone pocket of baz2a using ftmap to probe the apo crystal structure. ftmap readily identified the histone pocket as a hit (c), even though it perceived it as a borderline druggable pocket likely requiring charged compounds, […]

PMCID: 5869234
PMID: 29118093
DOI: 10.1042/EBC20170028

[…] one area that has received considerable attention in recent years is using molecular simulation methods to map the protein surface for which functional groups will bind, such as the programs ftmap [] and mdmix []. these can be seen as an extension of the earlier grid [] and mcss [] methods, but incorporating flexibility into the protein target and exploiting the massive increase […]

PMCID: 5618543
PMID: 28869519
DOI: 10.3390/ijms18091894

[…] may differ from the other cxcr1/2 chemokine ligands, and that sulfotyrosine may help cxcr1 discriminate between cxcl5 and cxcl8., previous computational solvent mapping of cxcl12 and ccl21 using ftmap identified sulfotyrosine recognition sites as hot spots for ligand binding [,]. the ftmap algorithm surveys the protein surface with 16 small organic molecule probes, then clusters and ranks […]

PMCID: 5556075
PMID: 28808284
DOI: 10.1038/s41598-017-08747-8

[…] where nonpolar and aromatic side chains impose specific prerequisites on drug size and shape. to further establish this, we performed a fragment based binding site characterization using ftmap, whose philosophy retraces experimental high-throughput and fragment screening methods. also, as its algorithm does not rely on alternate measures of ligand-binding propensity such as pocket […]


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FTMAP institution(s)
Program in Bioinformatics, Boston University, Boston, MA, USA

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