Dor O, Zhou Y (March 2007). “Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training”. Proteins66 (4): 838–45. doi:10.1002/prot.21298. PMID17177203.
Chou PY, Fasman GD (January 1974). “Prediction of protein conformation”. Biochemistry13 (2): 222–45. doi:10.1021/bi00699a002. PMID4358940.
Garnier J, Osguthorpe DJ, Robson B (March 1978). “Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins”. Journal of Molecular Biology120 (1): 97–120. doi:10.1016/0022-2836(78)90297-8. PMID642007.
Pham TH, Satou K, Ho TB (April 2005). “Support vector machines for prediction and analysis of beta and gamma-turns in proteins”. Journal of Bioinformatics and Computational Biology3 (2): 343–58. doi:10.1142/S0219720005001089. PMID15852509.
Zhang Q, Yoon S, Welsh WJ (May 2005). “Improved method for predicting beta-turn using support vector machine”. Bioinformatics21 (10): 2370–4. doi:10.1093/bioinformatics/bti358. PMID15797917.
Zimmermann O, Hansmann UH (December 2006). “Support vector machines for prediction of dihedral angle regions”. Bioinformatics22 (24): 3009–15. doi:10.1093/bioinformatics/btl489. PMID17005536.
Kuang R, Leslie CS, Yang AS (July 2004). “Protein backbone angle prediction with machine learning approaches”. Bioinformatics20 (10): 1612–21. doi:10.1093/bioinformatics/bth136. PMID14988121.
Costantini S, Colonna G, Facchiano AM (April 2006). “Amino acid propensities for secondary structures are influenced by the protein structural class”. Biochemical and Biophysical Research Communications342 (2): 441–51. doi:10.1016/j.bbrc.2006.01.159. PMID16487481.
Marashi SA, Behrouzi R, Pezeshk H (January 2007). “Adaptation of proteins to different environments: a comparison of proteome structural properties in Bacillus subtilis and Escherichia coli”. Journal of Theoretical Biology244 (1): 127–32. doi:10.1016/j.jtbi.2006.07.021. PMID16945389.
Costantini S, Colonna G, Facchiano AM (October 2007). “PreSSAPro: a software for the prediction of secondary structure by amino acid properties”. Computational Biology and Chemistry31 (5–6): 389–92. doi:10.1016/j.compbiolchem.2007.08.010. PMID17888742.
Adamczak R, Porollo A, Meller J (May 2005). “Combining prediction of secondary structure and solvent accessibility in proteins”. Proteins59 (3): 467–75. doi:10.1002/prot.20441. PMID15768403.
Shaw DE, Dror RO, Salmon JK, Grossman JP, Mackenzie KM, Bank JA, Young C, Deneroff MM, Batson B, Bowers KJ, Chow E (2009). Millisecond-scale molecular dynamics simulations on Anton. Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis - SC '09. p. 1. doi:10.1145/1654059.1654126. ISBN9781605587448。
Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (July 2016). “Coarse-Grained Protein Models and Their Applications”. Chemical Reviews116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. PMID27333362.
Göbel U, Sander C, Schneider R, Valencia A (April 1994). “Correlated mutations and residue contacts in proteins”. Proteins18 (4): 309–17. doi:10.1002/prot.340180402. PMID8208723.
Taylor WR, Hatrick K (March 1994). “Compensating changes in protein multiple sequence alignments”. Protein Engineering7 (3): 341–8. doi:10.1093/protein/7.3.341. PMID8177883.
Jin, Shikai; Chen, Mingchen; Chen, Xun; Bueno, Carlos; Lu, Wei; Schafer, Nicholas P.; Lin, Xingcheng; Onuchic, José N. et al. (9 June 2020). “Protein Structure Prediction in CASP13 Using AWSEM-Suite”. Journal of Chemical Theory and Computation16 (6): 3977–3988. doi:10.1021/acs.jctc.0c00188. PMID32396727.
Ponder JW, Richards FM (February 1987). “Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes”. Journal of Molecular Biology193 (4): 775–91. doi:10.1016/0022-2836(87)90358-5. PMID2441069.
Bower MJ, Cohen FE, Dunbrack RL (April 1997). “Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool”. Journal of Molecular Biology267 (5): 1268–82. doi:10.1006/jmbi.1997.0926. PMID9150411.
Voigt CA, Gordon DB, Mayo SL (June 2000). “Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design”. Journal of Molecular Biology299 (3): 789–803. doi:10.1006/jmbi.2000.3758. PMID10835284.
Dor O, Zhou Y (March 2007). “Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training”. Proteins66 (4): 838–45. doi:10.1002/prot.21298. PMID17177203.
Chou PY, Fasman GD (January 1974). “Prediction of protein conformation”. Biochemistry13 (2): 222–45. doi:10.1021/bi00699a002. PMID4358940.
Garnier J, Osguthorpe DJ, Robson B (March 1978). “Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins”. Journal of Molecular Biology120 (1): 97–120. doi:10.1016/0022-2836(78)90297-8. PMID642007.
Pham TH, Satou K, Ho TB (April 2005). “Support vector machines for prediction and analysis of beta and gamma-turns in proteins”. Journal of Bioinformatics and Computational Biology3 (2): 343–58. doi:10.1142/S0219720005001089. PMID15852509.
Zhang Q, Yoon S, Welsh WJ (May 2005). “Improved method for predicting beta-turn using support vector machine”. Bioinformatics21 (10): 2370–4. doi:10.1093/bioinformatics/bti358. PMID15797917.
Zimmermann O, Hansmann UH (December 2006). “Support vector machines for prediction of dihedral angle regions”. Bioinformatics22 (24): 3009–15. doi:10.1093/bioinformatics/btl489. PMID17005536.
Kuang R, Leslie CS, Yang AS (July 2004). “Protein backbone angle prediction with machine learning approaches”. Bioinformatics20 (10): 1612–21. doi:10.1093/bioinformatics/bth136. PMID14988121.
Costantini S, Colonna G, Facchiano AM (April 2006). “Amino acid propensities for secondary structures are influenced by the protein structural class”. Biochemical and Biophysical Research Communications342 (2): 441–51. doi:10.1016/j.bbrc.2006.01.159. PMID16487481.
Marashi SA, Behrouzi R, Pezeshk H (January 2007). “Adaptation of proteins to different environments: a comparison of proteome structural properties in Bacillus subtilis and Escherichia coli”. Journal of Theoretical Biology244 (1): 127–32. doi:10.1016/j.jtbi.2006.07.021. PMID16945389.
Costantini S, Colonna G, Facchiano AM (October 2007). “PreSSAPro: a software for the prediction of secondary structure by amino acid properties”. Computational Biology and Chemistry31 (5–6): 389–92. doi:10.1016/j.compbiolchem.2007.08.010. PMID17888742.
Adamczak R, Porollo A, Meller J (May 2005). “Combining prediction of secondary structure and solvent accessibility in proteins”. Proteins59 (3): 467–75. doi:10.1002/prot.20441. PMID15768403.
Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (July 2016). “Coarse-Grained Protein Models and Their Applications”. Chemical Reviews116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. PMID27333362.
Göbel U, Sander C, Schneider R, Valencia A (April 1994). “Correlated mutations and residue contacts in proteins”. Proteins18 (4): 309–17. doi:10.1002/prot.340180402. PMID8208723.
Taylor WR, Hatrick K (March 1994). “Compensating changes in protein multiple sequence alignments”. Protein Engineering7 (3): 341–8. doi:10.1093/protein/7.3.341. PMID8177883.
Jin, Shikai; Chen, Mingchen; Chen, Xun; Bueno, Carlos; Lu, Wei; Schafer, Nicholas P.; Lin, Xingcheng; Onuchic, José N. et al. (9 June 2020). “Protein Structure Prediction in CASP13 Using AWSEM-Suite”. Journal of Chemical Theory and Computation16 (6): 3977–3988. doi:10.1021/acs.jctc.0c00188. PMID32396727.
Ponder JW, Richards FM (February 1987). “Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes”. Journal of Molecular Biology193 (4): 775–91. doi:10.1016/0022-2836(87)90358-5. PMID2441069.
Bower MJ, Cohen FE, Dunbrack RL (April 1997). “Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool”. Journal of Molecular Biology267 (5): 1268–82. doi:10.1006/jmbi.1997.0926. PMID9150411.
Voigt CA, Gordon DB, Mayo SL (June 2000). “Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design”. Journal of Molecular Biology299 (3): 789–803. doi:10.1006/jmbi.2000.3758. PMID10835284.