:: DESCRIPTION
DireX is a software to generate ensembles of protein structures that are in agreement with low resolution or sparse experimental data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
G.F.Schröder, A.T.Brunger, and M.Levitt
‘Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution‘
Structure, Vol 15, 1630-1641 (2007)
:: DESCRIPTION
RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit against the evolutionary group that the HMM models, and it does this using through iterative database searches and incremental subsequent adaptation of the seed set.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Oct 27;11:534. doi: 10.1186/1471-2105-11-534.
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement.
Hedlund J, Jörnvall H, Persson B.
:: DESCRIPTION
REFINER is an algorithm that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core model of a protein family.
::DEVELOPER
Computational Biophysics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2006 Nov 14;7:499.
State of the art: refinement of multiple sequence alignments.
Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.
:: DESCRIPTION
PTMClust is a software that can be applied to the output of blind PTM (Post-translational Modification) search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We showed that our technique outperforms two standard clustering algorithms on a simulated dataset. Additionally, we showed that our algorithm significantly improves sensitivity and specificity when applied to the output of three different blind PTM search engines, SIMS, InsPecT and MODmap. Additionally, PTMClust markedly outforms another PTM refinement algorithm, PTMFinder. We demonstrate that our technique is able to reduce false PTM assignments, improve overall detection coverage and facilitate novel PTM discovery, including terminus modifications. We applied our technique to a large-scale yeast MS/MS proteome profiling dataset and found numerous known and novel PTMs. Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Mar 15;27(6):797-806. Epub 2011 Jan 22.
Computational refinement of post-translational modifications predicted from tandem mass spectrometry.
Chung C, Liu J, Emili A, Frey BJ.
