PACSY-ALIGN Instructions

PACSY-ALIGN is a web server that provides useful information for efficient protein 3D structure determination.

It finds ten closest entries to your protein in the Protein Data Bank, analyzes structural properties, generates 3D-NOESY assignments.

The NOE assignments can be refined by new “Label” function in the Read Peak List window (two-letter-code: rp) of NMRFAM-Sparky. Distance constraints generated from the assignments (two-letter-code: gd or xf) and angle constraints from PACSY-ALIGN are already good for calculating your structure. Also, they guide automated NOE assignments in PONDEROSA-C/S and CYANA by providing global fold information from homologous relatives.

Input File:

• NMR-STAR 3.1 (BMRB) format

Output Files:

• Overall report for similar proteins

• Sequence alignment and structural analysis results towards PDB data

• Assignments of 2D and 3D-NOESY (15N/13C/Aro), and distance constraints

• Assignments of user 3D-NOESY (15N/13C/Aro), and distance constraints

• Extracted sequences from user input (1-letter, 3-letter formats)

• PECAN secondary structure prediction

• TALOS-N predicted torsion angle and RCI S2 prediction (PONDEROSA/CYANA/XPLOR format constraints)

Citation information