Citation information

PACSY-ALIGN is made possible by interfacing many others' contributions.

Please cite accordingly depending on your usage.

PACSY database for structure pool search

Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. PACSY, a relational database management system for protein structure and chemical shift analysis. J Biomol NMR. 2012 Oct;54(2):169-79

RCSB PDB for atomic coordinates

Berman HM, WestBrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research. 2000; 28:235-242

Sequence alignment (Smith-Watermann algorithm)

Smith TF, Waterman MS. Identification of Common Molecular Subsequences. J Mol Biol. 1981; 147: 195-197

PECAN secondary structure prediction

Eghbalnia HR, Wang L, Bahrami, A, Assadi A, Markley JL. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR. 2005 May;32(1):71-81

TALOS-N torsion angle prediction

Shen Y, Bax A. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR. 2013; 56:227-241

Random Coil Index (RCI) S2 order parameter

Berhanskii MV, Wishart DS. A simple method to predict protein flexibility using secondary chemical shifts. JACS. 2005; 127:14970-14971

PONDEROSA-C/S for NOESY simulation

Lee W, Stark JL, Markley JL. PONDEROSA-C/S: Client-server based software package for automated protein 3D structure determination. J Biomol NMR 2014; 60(2-3):73-5

NMRFAM-SPARKY for validating simulated NOESY (two-letter-code: rp)

Lee W, Tonelli M, Markley JL. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12