Research references

Chou PY (1990). "Prediction of protein structural classes from amino acid composition." In Prediction of Protein Structure and the Principles of Protein Conformation, Plenum Press, New York, NY, pp. 549-586.

Chou PY and Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence." Advances in Enzymology 47: 45-148.

Claros MG and von Heijne G (1994). "TopPred II: An Improved Software For Membrane Protein Structure Predictions." Comput. Appl. Biosci. 10(6): 685-686. [Reference pertains to Protean 3D’s TopPred algorithm].

Deléage G and Roux B (1987). "An algorithm for protein secondary structure prediction based on class prediction." Protein Engineering 1: 289-294.

Deveaud and Schuerer (Pasteur Institute). "New implementation of the original TopPred program, based on the G. von Heijne algorithm."

Eisenberg D, Weiss RM and Terwilliger TC (1984). "The hydrophobic moment detects periodicity in protein hydrophobicity." Proceedings of the National Academy of Science (USA), 81(1): 140-144.

Emini EA, Hughes J, Perlow D and Boger J (1985). "Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide." Journal of Virology, 55: 836-839.

Engleman DM, Steitz TA and Goldman A (1986). "Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins." Annual Review of Biophysics and Biophysical Chemistry, 15: 321-54.

Garnier J, Gibrat JF, Robson B (1996). "GOR method for predicting protein secondary structure from amino acid sequence." Methods Enzymol. 266:540-53. [Reference pertains to Protean 3D’s GOR IV algorithm].

Garnier J, Osguthorpe DJ and Robson B (1978). "Analysis of the accuracy and implications of simple method for predicting the secondary structure of globular proteins." Journal of Molecular Biology, 120: 97-120. [Reference pertains to Protean 3D’s Garnier-Robson method].

Garnier J and Robson B (1990). "The GOR Method for Predicting Secondary Structures in Proteins." In Prediction of Protein Structure and the Principles of Protein Conformation, ed. G.D. Fasman (2nd ed). Plenum Press, New York. [Reference pertains to Protean 3D’s GOR II algorithm].

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD and Bairoch A (2005). "Protein Identification and Analysis Tools on the ExPASy Server." In The Proteomics Protocols Handbook, ed. John M. Walker, Humana Press, pp. 571-607.

Gill SC and von Hippel PH (1989). "Calculation of protein extinction coefficients from amino acid sequence data." Analytical Biochemistry, 182: 319-326.

Guruprasad K, Reddy BVB and Pandit MW (1990). "Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence." Protein Eng., 4, 155 – 161.

Hopp TP and Woods KR (1981). "Prediction of protein antigenic determinants from amino acid sequences." Proceedings of the National Academy of Science, 78: 3824-3828.

Jameson BA and Wolf H (1988). "The antigenic index: a novel algorithm for predicting antigenic determinants." CABIOS, 4: 181-186.

Kabsch W and Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features." Biopolymers, 22: 2577-2637.

Karplus PA and Schultz GE (1985). "Prediction of chain flexibility in proteins." Naturwissenschaft, 72: 212-213.

Krebs WG and Gerstein M (2000). “The Morph Server: A standardized system for analyzing and visualizing macromolecular motions in a database framework.” Nucleic Acids Res 28: 1665-75. [Pertains to the Motion Library.]

Kyte J and Doolittle RF (1982). "A simple method for displaying the hydropathic character of a protein." Journal of Molecular Biology, 157: 105-132.

Lathrop RH, Webster TA, and Smith TF (1987). “Ariadne: Pattern-directed inference and hierarchical abstraction in protein structural recognition.” Communications of the ACM 30: 909-921. [Pertains to Ariadne patterns.]

Lehninger A (2005). Principles of Biochemistry, 4th Edition, Chapter 3, page 78, Table 3-1.

Lehninger A, Nelson D, and Cox M (2005). “Principles of biochemistry.” New York: W.H. Freeman.

Lupas A, Van Dyke M and Stock J (1991). "Predicting coiled coils from protein sequences." Science 252: 1162-1164.

Margalit H, Berzofsky J et al. (1987). "Prediction of immunodominant helper T cell antigenic sites from the primary sequence." Journal of Immunology, 138: 2213-2229.

Mariani V, Biasini M, Barbato A, Schwede T (2013). lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics. 2013 Nov 1;29(21):2722-8. doi: 10.1093/bioinformatics/btt473.

Nakashima H, Nishikawa K and Ooi T (1986). “The folding type of a protein is relevant to the amino acid composition.” Journal of Biochemistry (Tokyo), 99: 153-162.

Parker JMR, Guo D and Hodges RS (1986). “New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: Correlation of predicted surface residues with antigenicity and x-ray-derived accessible sites.” Biochemistry, 25: 5425-5432.

Parry DA (1982). “Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins.” Biosci Rep. 1982 Dec;2(12):1017-24.

Pierce NA, Spriet JA, Desmet J, Mayo SL. (2000) “Conformational splitting: A more powerful criterion for dead-end elimination.” J Comput Chem. 21:999-1009.

Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A and Bourne PE (2010). “Precalculated Protein Structure Alignments at the RCSB PDB website.” Bioinformatics. 26(23):2983-5.

Ren J et al. (2009). “Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0.”“Proteomics, 9: 3409-3412.

Rothbard JB and Taylor WR (1988). “A sequence pattern common to T cell epitopes.” EMBO Journal, 7: 93-100.

Sasagawa T, Okuyama T and Teller D (1982). “Prediction of peptide retention times in reversed-phase high-performance liquid chromatography during linear gradient elution.” Journal of Chromatography, 240: 329-340.

Sette A et al. (1989). “Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis.” Proceedings of the National Academy of Science, 86: 3296-3300.

Troshin PV, Procter JB and Barton GJ (2011). “Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment – JABAWS:MSA.” Bioinformatics; doi: 10.1093/bioinformatics/btr304.

von Heijne G (1981). “On the hydrophobic nature of signal sequences.” Eur. J. Biochem., 116: 419-422. [Reference pertains to Protean 3D’s von Heijne method].

von Heijne G (1992). “Membrane Protein Structure Prediction: Hydrophobicity Analysis and the ‘Positive Inside’ Rule.” J. Mol. Biol. 225(2): 487-494. [Reference pertains to Protean 3D’s TopPred algorithm].

Webster TA, Lathrop RH., and Smith TF (1987). “Prediction of a common structural domain in aminoacyl-trna synthetases through use of a new pattern-directed inference system.” Biochemistry 26: 6950-6957. [Pertains to Ariadne patterns.]

Webster TA, Tsai H, Kula M, Mackie GA and Schimmel PR (1984). “Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthase.” Science 226: 1315-1317. [Pertains to Ariadne patterns.]

Welling GW, Weijer WJ, van der Zee R and Welling-Wester S (1985). “Prediction of sequential antigenic regions in proteins.” FEBS Letters, Vol. 188, No. 2: 215-218.

White A, Handler P and Smith E (1964). Principles of Biochemistry, 3rd Edition, p. 124.

Xu D and Zhang Y (2009). “Generating triangulated macromolecular surfaces by Euclidean Distance Transform.” PLoS One 4(12):e8140. [Reference pertains to Protean 3D’s EDTSurf algorithm].

Yang ZR, Thomson R, McMeil P and Esnouf RM (2005). RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21: 3369-3376.

Ye Y and Godzik A. (2003) “Flexible structure alignment by chaining aligned fragment pairs allowing twists.” Bioinformatics. 19 Suppl 2:ii246-55.

Zhang Y and Skolnick J (2005). “TM-align: a protein structure alignment algorithm based on the TM-score.” Nucleic Acids Res. 33(7):2302-9. [Reference pertains to Protean 3D’s TM-align algorithm].