Fit RDCs to a Structure
Using Non-Linear Least Squares
Calculate RDCs for a Structure
Using Known Order Matrix Parameters
Using Known Alignment Tensor Parameters
Calculate General Classes of RDCs for a Structure
Generate Randomly Oriented HN-N Atom Pairs
Secondary Structure Prediction (Sequence Based)
Poulsen IDP/IUP Random Coil Chemical Shifts
Bax's Group @NIH
From the Bax Group at the National Institutes of Health
System for Chemical Shifts Based Protein Homology Modeling
Chemical shift guided homology modeling of larger proteins, Yang Shen, Ad Bax, Nat. Methods, 2015 (in press). [
POMONA Web Site:
Chemical Shift Input
Upload a Chemical Shift File
Chemical Shift Format
BMRB NMRSTAR V2.1
BMRB NMRSTAR V3.1
The input table of chemical shifts and sequence information. The format of the table is described in the
TALOS Web Page.
As an alternative, the input table of chemical shifts and sequence information can be specified as a
BMRB NMR-Star format
(v2.1 or v3.1) file.
In order to use NMRSTAR format as input to POMONA & CS-RosettaCM, the BMRB file should have chemical shift information and complete sequence information for a single protein only. When input is supplied as a BMRB file, CYS residues with a CB shift of 34ppm or less are assumed to be reduced, and HIS residues in tables with a listed pH of 6.0 or less are assumed to be protonated.
TALOS Format (ubiq.tab)
NMRStar V2.1 Format (ubiq.str)
NMRStar V3.1 Format (bmr6457.str)
Select this option to test the input chemical shift referencing and apply an automated offset correction if needed.
Deuterium Correction (Deuterated Proteins Only)
. Select this option if the input CA and CB chemical shifts need to be adjusted for deuterium isotope effect. Leave this option off if you have already adjusted the CA and CB shifts.
Trim Flexible Tails
Select this option to automatically identify and trim flexible talis by using a RCI-S2 cutoff of 0.65.
Warning: All tail resisdues without chemical shift assignments will be assigned as flexible by this automatic procedure. If it is not the fact, users can use the other option to manually specify the flexible residues.
Use this option to specify the flexible residues to be trimmed, with a separator of a space character.
Choose Search Set
All PDB Proteins
Select this option to search all proteins in PDB
Selected PDB Protein(s)
Select this option to specify the protein(s) to be aligned. Proteins should be listed with a seperator of a space character and with a format of 4-letter PDB identifier plus a 1-letter chain id, such as:
1ubqA 1d3zA 2oedA
Max. Allowed Sequence Identity
Specify in this option the sequence identity value if sequence homologues in the database need to be excluded, with an allowed range of 0.0-100.0
Specify in this option the proteins that need to be excluded, all proteins should be listed by a seperator of a space and with a format of 4-letter PDB identifier plus a 1-letter chain id, such as:
1ubqA 1d3zA 2oedA
Click [+] to view or change the default settings. Note that the default alignment settings will fulfill the needs of most users
Chemical Shift Similiarity
Specify in this option the weight of chemical shift matching score used to calculate an alignment score, with an allowed range of 0.0-1.0
Amino Acid Similiarity
Specify in this option the weight of amino acid similarity score used to calculate an alignment score, with an allowed range of 0.0-1.0
Gap Opening Penalty
Specify in this option the gap opening penalty used by alignment procedure, with an allowed range of 0.0-100.0
Gap Extension Penalty
Specify in this option the gap extension penalty used by alignment procedure, with an allowed range of 0.0-100.0
Max. Number of Positive Hits
Specify in this option the max. number of positive aliggments returned by POMONA, with an allowed range of 10-2000
Generate CS-RosettaCM Inputs
Select this option to generate a package of inputs for running a RosettaCM full atom modeling, which includes: RosettaCM scripts and required scoring files, de novo fragments (selected with chemical shifts), strucutre templates from Pomona alignments
Template Selection Options
Num. of Selected Top Clusters
Select this option to specify the number of top POMONA clusters selected to generate template inputs for CS-RosettaCM full atom modeling, with an allowed range of 1-100.
Num. of Alignments per Cluster
Select this option to specify the number of POMONA alignments per cluster selected to generate template inputs for CS-RosettaCM full atom modeling, with an allowed range of 1-100.
Note: attachments with large size (~20MB for 300-residue proteins) will be sent via email, make sure your email can receive such files!
Calculation results will be sent via Email only. Email Address should not contain special characters.
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last update: Apr 6, 2015