LACS is an automated tool for assignment outlier detection and correction of errors in referencing.

BACKGROUND

MANUAL

EXAMPLES

CITATION

Liya Wang, Hamid R. Eghbalnia, Arash Bahrami, John L. Markley; "Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications"; Journal of Biomolecular NMR, 2005 May;32(1):13-22.

 

LACS is an automated tool for assignment outlier detection and correction of errors in referencing. The input format is NMRSTAR 2.1 (BMRB) format, and. the result will be returned via email in a couple of minutes. Expand the "SUBMISSION" tab below for free access to the LACS analysis web-server maintained by NMRFAM.

BACKGROUND

The process of assigning a finite set of tags or labels to a collection of observations, subject to side conditions, is notable for its computational complexity. This labeling paradigm is of theoretical and practical relevance to a wide range of biological applications, including the analysis of data from DNA microarrays, metabolomics experiments, and biomolecular nuclear magnetic resonance (NMR) spectroscopy. We present a novel algorithm, called Probabilistic Interaction Network of Evidence (PINE), that achieves robust, unsupervised probabilistic labeling of data. The computational core of PINE uses estimates of evidence derived from empirical distributions of previously observed data, along with consistency measures, to drive a fictitious system M with Hamiltonian H to a quasi-stationary state that produces probabilistic label assignments for relevant subsets of the data. We demonstrate the successful application of PINE to a key task in protein NMR spectroscopy: that of converting peak lists extracted from various NMR experiments into assignments associated with probabilities for their correctness. This application, called PINE-NMR, is available from a freely accessible computer server (http://pine.nmrfam.wisc.edu). The PINE-NMR server accepts as input the sequence of the protein plus user-specified combinations of data corresponding to an extensive list of NMR experiments; it provides as output a probabilistic assignment of NMR signals (chemical shifts) to sequence-specific backbone and aliphatic side chain atoms plus a probabilistic determination of the protein secondary structure. PINE-NMR can accommodate prior information about assignments or stable isotope labeling schemes. As part of the analysis, PINE-NMR identifies, verifies, and rectifies problems related to chemical shift referencing or erroneous input data. PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination.  

SUBMISSION

Access the PINE webserver submission form here.  

MANUAL

 

NMR-STAR input supported by MANI-LACS

Input

The format for  input supported by MANI-LACS is shown below.  The input format is the portion of the NMR-STAR file format that describes the chemical shift information.   The NMR-STAR file (http://www.bmrb.wisc.edu) MUST contain both sequence and shifts.
 

 Please do not remove any of the words:
   _Mol_residue_sequence ,  loop
   _Chem_shift_ambiguity_code, etc..
   can NOT be removed
The example below illustrates the fomat.
   ...........................................................
    _Mol_residue_sequence
   ;
   MKSTGIVRKVDELGRVVIPI
   ELRRTLGIAEKDALEIYVDD
   EKIILKKYKPNMT
   ;
   loop_
   _Residue_seq_code
   _Residue_label
   _Chem_shift_ambiguity_code
   4    2   LYS  HG2   H    1.61  .  2
   5    2   LYS  HD2   H    1.40  .  2
   6    2   LYS  HE2   H    2.91  .  2
   -stop
   ...................

CITATION

 Liya Wang, Hamid R. Eghbalnia, Arash Bahrami, John L. Markley, "Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications", Journal of Biomolecular NMR, 2005 May;32(1):13-22.