Update (12) RC1 release (7th June 2010)
updated bug-tracking system
FASTA module has been temporarily disabled
Update (11) RC1 release (3rd June 2010)
minor help system corrections
minor HTML footer formatting corrections
Update (10) RC1 release (10th May 2010)
minor HTML formatting corrections
revision of help pop-up system
revision of JTrac / Bug Reports
Update (9) RC1 release (23rd April 2010)
updated server configuration files for improved performance
added new method: RefDB chemical shifts by Zhang et al. (2003)
Update (8) RC1 release (30th Mar 2010)
added ASCII-formatted output for ncSPC calculations
Update (7) RC1 release (15th Feb 2010)
added ASCII-formatted secondary chemical shifts
Update (6) RC1 release (8th Feb 2010)
restored original SSP settings (according to Marsch et. al 2006)
Update (5) RC1 release (2nd Feb 2010)
calculation process speeded up by elimination of unnecessary options, now consists of 3-selection screens
solved issue with incomplete treatment of HA data, due to HA2/HA3 IPUC naming conventions for GLY residues; if more than one HA assignment is available standard average HA is used
experimental vs predicted fit plots are annotated with a blue dashed f(x) = x line
ncSPC plots are done in the "classical" way which speeds up the rendering process and improves the responsiveness of the user interface
more information about retrieved BMRB entry can be obtained via link to the BMRB summary record
added "window size" option for a moving average filter
fixed annoying problem with "disappearing" SSP/ncSPC plots for 15N scores, primarily observed with BMRB 4402
Update (4) RC1 release (18th Jan 2010)
removed author/journal/year fields from the Session Summary, due to faulty processing of some selected NMR STAR files
Update (3) RC1 release (13th Jan 2010)
corrected a small bug in random-coil chemical shift computation module
Update (2) RC1 release (16th Dec 2009)
added custom HTML Error Pages: 401, 403, 404
added gradient coded ncSPC graphs
Update (1) RC1 release (23rd Nov 2009)
updated IDP "random-coil" database
RC1 release (3rd Nov 2009)
enable mod_deflate compression of web contents (56% speed up of loading times)
added custom ncSPC favicon
added Intrinsic Structural Propensity Calculation Module
ncSPC goes on-line!
added extensive usage statistics using Webalizer 2.01
verified and corrected ncSPC/SSP score "overshooting" and restored 1.2 as a default max. score
corrected wrong weighting factor for alpha/beta scores in ncSPC for 1HN
general disorder score is weighted by the intrinsic chemical dispersion values
minor style corrections/enhancements for the general display and help system
as requested by users in WISH-5 ticket: an extensive calculation summary is provided
fixed issues reported by users in DPI-11 ticket: color code for graphs should be consistent by now
fixed a problem reported by users in STEP1-4 ticket: reverting all steps back and pressing initial submit button generates an error
fixed a problem reported by users in DPI-12 ticket: submitting calculation without any option selected
as requested in COMP-11 ticket: manual reference offset correction option is now available both for BMRB ID and STAR file
fixed an issue reported by users in COMP-13 ticket: abnormal behaviour of ncSPC tool with 6078 BMRB entry
fixed an issue reported by users in COMP-12 ticket: abnormal ncSPC termination upon BMRB 7279 processing with Z-score re-referencing on
as requested by users in COPM-10 ticket: fitting routine uses f(x)=x+b function instead of f(x)=ax+b
as requested by users changed relative scaling of SSP and ncSPC plots from +/- 1.0 to +/- 1.2
concerning WISH-3 ticket: ncSPC 1.5b is compatible with an intermediate BMRB file (STAR 3.1) compliant produced by CCPN Format Converter Tool
1.4b release (29th Sep 2009)
fixed issue reported by users in DPI-9/DPI-10 ticket: malfunctioning "Restart Calculations" button
concerning the WISH-3 ticket: a link to the Online CCPN File Format Converter Interface has been added. User can convert and more importantly
validate NMR assignment tables. Multiple file formats are available. For further details please consult CCPN Format Converter Interface
added 2H isotope shift corrections for 13CA and 13CB nuclei (courtesy of Drs. Renee Otten)
minor button style corrections
fixed issue reported by users in COMP-9 ticket: abnormal termination of ncSPC 1.3B upon manual file upload and Z-score based 13CA/13CB re-referencing
1.3b release (25th Sep 2009)
fixed issue reported by users in COMP-5 ticket: added missing square root in the RMSD equation
as suggested by users in WISH-1 ticket: changed x-axis scaling from -5/5 ppm to +/- 4*sigma (standard deviation) of secondary chemical shifts
verified and explained issue reported by users in STEP1-3 ticket: the problem of independent calculations using multi-tabbed browsing with only one
instance of the browser running
as requested in WISH-2 ticket : added raw secondary chemical shift graphs and reported mean values of secondary shifts
some minor style/interface enhancements
as suggested in COMP-6 ticket: N/C-termini are excluded from the SSP/ncSP calculations
corrected easy to spot typographic errors
modified Z-score 13CA/13CB re-referencing algorithm: if calculated offset value is smaller than RefDB threshold offset +/- 0.2ppm, 13CA/13CB shifts are not re-referenced.
verified and explained issue reported by users in COMP-8 ticket: suspicious 13CO shifts in 1-10 fragment of BMRB ID 6457 entry
verified and fixed COMP-4 issue: all random-coil shifts are produced in sorted/coherent order
verified and fixed COMP-7 issue: missing entries in original implementation of SSP have been added. Standard SSP module produces all graphs
1.2b release (23rd Sep 2009)
added Z-score 13C re-referencing algorithm (applies to 13CA and 13CB nuclei) according to: Marsh et al. Protein Science (2006)
added secondary chemical shift computation module and formatted ACSII output
added linear regression analysis graphs for predicted vs experimental data
fixed issues reported by users in DPI-8 ticket
fixed issues reported by users in DPI-7 ticket
fixed issues reported by users in STEP3-2 ticket: it is possible to make a selection of all options using only single checkbox
STEP[3] Option selection panel has been divided into subsections
fixed an issue with improper relative weighting of secondary chemical shifts in ncSP module which was leading to routinely underestimated scores
modified server load display: the status of two CPUs is displayed as an horizontal bar with the color code indicating current load
extended input data exception handling, input files/BMRB ID are thoroughly checked and searched for assignment data
enabled "classical" SSP calculation module, adapted from Marsh et al. Protein Science (2006)
1.1b release (21th Sep 2009)
added support for FancyBox display library for clear viewing of graphs
calculation session starts with input data selection page, offering 3 different types of input: via BMRB ID, via file upload and via FASTA sequence
small user interface tweaks/style corrections
new icon set for results panel and buttons
corrected formatting of random coil chemical shift output
added Change-log panel in main menu
1.0b release (17th Sep 2009)
retrieve and process NMR data directly from BMRB database
manually upload and process NMR data in STAR 2.x/3.x format
generate neighbor corrected random coil chemical shifts
compare experimental vs predicted data: fit with a(x)+b function
compare experimental vs predicted data: generate secondary chemical shift histograms
compare experimental vs predicted data: generate chemical shift RMSD
calculate neighbor corrected Structural Propensity plots
create multiple output files