Software external to NYSBC

NMR

Automated assignment and assignment checking

• http://bija.nmrfam.wisc.edu/PISTACHIO/ PISTACHIO offers fully automatic backbone and sidechain assignments using a new approach to assignment that achieves excellent results.
• http://bija.nmrfam.wisc.edu/PECAN/ PECAN offers a new approach to secondary structure identification that achieves excellent results.
• NmrView

Format and interconversion issues

• CCPN Format converter

Academic development centers

Wuthrich Lab

• Cara project

1. Documentation http://www.cara.nmr-software.org/downloads/
2. local copy of Win 32 program -- see the attachement list below
3. local copy of linux program -- see the attachment list below

Bax group

• NEW -- TALOS+ -- LIBRARY:ShenDelaglio09.pdf -- Talos+ download and notes

Structure Calculation

• CyanA
• See Amber this page

Commercial suppliers

• Bruker
• http://www.las.jp/index_eg.html L.A. Systems (CyanApg1 etc. )

Lists of lists

• Spincore
• http://web.mit.edu/speclab/www/software.htm

Molecular

• http://amber.scripps.edu/ Amber home page
• See the CEM installations at CemIT

---+Internal features

Fitting a single Kd to multiple shift titration data - NmrTitration

1. Needed data - 1. protein concentration at start. 2. initial total volume, 3 concn of ligand in the added volumes , 4 incremental volume added , 5 number of increments (VS), 6 number of peaks logged (VN), 7 matrix of shifts (VS, VN)
2. assumes multiple equal steps. Can be altered to use none equal volumes.
3. Precision is limited by VS and VN and the relative Kd.

Predicting good dipeptide pairs for selective labeling - NmrDipep

1. Demo script -
2. Needed data -

-- DavidCowburn - 07 Sep 2004