The FANDAS 2.0 web server
About FANDAS 2.0: Fast Analysis of multidimensional NMR DAta Sets (FANDAS) is a tool to predict peaks for multidimensional NMR experiments on proteins. FANDAS accepts a variety of inputs, with the protein sequence being the only minimum required input. The output generated by FANDAS can be opened using the NMR visualization software: SPARKY. Description of all the features that FANDAS offers is described in our publication mentioned below.
To cite FANDAS 2.0:
1) S. Gradmann, C. Ader, I. Heinrich, D. Nand, M. Dittmann, A. Cukkemane, M. van Dijk, A.M.J.J. Bonvin, M. Engelhard and M. Baldus "Rapid prediction of multi-dimensional NMR data sets." J. Biomol. NMR, 54, 377-387 (2012).
2) S. Narasimhan, D. Mance, C. Pinto, M. Weingarth, A.M.J.J. Bonvin and M. Baldus "Rapid prediction of multi-dimensional NMR data sets using FANDAS." Methods in Molecular Biology (submitted)
Download FANDAS 2.0 Python Application
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>>Input Sequence and Secondary Structure

Project Name*: No spaces or special characters (except "_")
NOTE: If you use an existing name, the files will be overwritten
Protein Sequence (single letter amino acid code)*
Secondary Structure without spaces, like the sequence
'a'= alpha helix 'b'= beta sheet 'c' = random coil 'n' = BMRB averages updated (21/08/2016)
>>Input Chemical Shifts as BMRB Tables

Recommended format- space delimited NMR-STAR (any version)
Hint: You can use packages such as SHIFTX2 to predict chemical shifts for a given PDB structure
Format example: 1 1 TRP HD1 H 7.33 0.01 1
Provide column number (starting with 1) for:
Residue number:   Atom name:   Chemical shift:
Provide residue number for first entry to match the sequence (to renumber the residue numbers in the list):
>>Amino Acid Selective Labelling Schemes

Select a labelling scheme
Reverse labelling scheme (would remove the amino acids entered below)
12C & 14N- List:    12C- List:    14N- List: Separate the amino acids by a space
Forward labelling scheme (would label only the amino acids entered below)
13C & 15N- List:    13C- List:    15N- List: Separate the amino acids by a space
Fully labelled (Default)
>>Glycerol Labelling Schemes & Fractional Deuteration

NOTE: Glycerol labelling cannot be coupled with amino acid selective labelling schemes, choosing the former would disable the latter and vice-versa
1,3-Glycerol  2-Glycerol  Follow this link for description
Fully labelled  (Default)

Fractionally Deuterated

Follow this link for description
>>Distance List Between Homonuclear (H-H or C-C) Pairs

Hint: You can use our Python Script to create such a list from a PDB
Format syntax: resi_num_1, atm_name_1, resi_num_2, atm_name_2, dist (in Å)
Format example: 1, CA, 3, CB, 15
Distance cut-off (in Å):
>>Predict Peaks for NMR Experiments (SPARKY format)

Peak Labels On    Off
Offset residue numbers in the peak file to start with residue number
Atoms within the brackets represent that they are not seen in the spectrum
2D NMR Experiments
N-H H-N C-H
H-C H-H Spin Diffusion C-C DQ-SQ Correlation
C-C Spin Diff. intra residue C-C Spin Diff. (residues i, i+1 & i-1) N-Cα
N-Co N-(Cα)-Cx N-(Cα)-Cx (residues i, i+1 & i-1)
N-(Co)-CαCb N-(Co)-Cx Cα-(N)-H
Co-(N)-H Cα-(Co)-(N)-H Co-(Cα)-(N)-H
N-(Cα)-H Cβ-(Cα)-(N)-H Cβ-(Cα)-(Co)-(N)-H
3D NMR Experiments
N-Cα-Cx N-Cα-Cx (residues i, i+1 & i-1) N-Co-Cx
N-Co-CαCb SQSQSQ (residues i, i+1 & i-1) DQSQSQ intra residue
DQSQSQ (residues i, i+1 & i-1) Cα-N-H Co-N-H
Cα-(Co)-N-H Co-(Cα)-N-H N-Cα-Hα
Cβ-(Cα)-N-H Cβ-(Cα)-(Co)-N-H

2D NMR Experiments (Distance Encoded)
C-C Spin Diffusion H-H Spin Diffusion C-(HH)-C
N-(HH)-C C-(H)-H N-(H)-H
N-(Cα)-Cx N-(Co)-Cx

3D NMR Experiments (Distance Encoded)
N-Cα-Cx N-Co-Cx C-H-H
N-H-H


Results will be stored for upto a day