| [1] | Domingues FS, Koppensteiner WA, Sippl MJ (2000) The role of protein structure in genomics. FEBS Lett 476: 98–102.
|
| [2] | Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294: 93–96.
|
| [3] | Cozzetto D, Tramontano A (2008) Advances and pitfalls in protein structure prediction. Curr Protein Pept Sci 9: 567–577.
|
| [4] | Petrey D, Honig B (2005) Protein structure prediction: inroads to biology. Mol Cell 20: 811–819.
|
| [5] | Simons KT, Bonneau R, Ruczinski I, Baker D (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl 3: 171–176.
|
| [6] | Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5: 725–738.
|
| [7] | Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5: 17.
|
| [8] | Zhang Y, Arakaki AK, Skolnick J (2005) TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 61 Suppl 791–98.
|
| [9] | Zhang J, Wang Q, Barz B, He Z, Kosztin I, et al. (2010) MUFOLD: A new solution for protein 3D structure prediction. Proteins 78: 1137–1152.
|
| [10] | Lazaridis T, Karplus M (1999) Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 288: 477–487.
|
| [11] | Petrey D, Honig B (2000) Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci 9: 2181–2191.
|
| [12] | Wu Y, Lu M, Chen M, Li J, Ma J (2007) OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Sci 16: 1449–1463.
|
| [13] | Yang Y, Zhou Y (2008) Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins 72: 793–803.
|
| [14] | Lassmann T, Sonnhammer EL (2005) Automatic assessment of alignment quality. Nucleic Acids Res 33: 7120–7128.
|
| [15] | Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12: 1073–1086.
|
| [16] | Gao X, Bu D, Li SC, Xu J, Li M (2007) FragQA: predicting local fragment quality of a sequence-structure alignment. Genome Inform 19: 27–39.
|
| [17] | Ray A, Lindahl E, Wallner B (2012) Improved model quality assessment using ProQ2. BMC Bioinformatics 13: 224.
|
| [18] | Benkert P, Tosatto SC, Schwede T (2009) Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins 77 Suppl 9173–180.
|
| [19] | Zemla A (2003) LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 31: 3370–3374.
|
| [20] | Moult J, Pedersen JT, Judson R, Fidelis K (1995) A large-scale experiment to assess protein structure prediction methods. Proteins 23: ii-v.
|
| [21] | Wang Q, Vantasin K, Xu D, Shang Y (2011) MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction. Proteins 79 Suppl 10185–195.
|
| [22] | Cheng J, Wang Z, Tegge AN, Eickholt J (2009) Prediction of global and local quality of CASP8 models by MULTICOM series. Proteins 77 Suppl 9181–184.
|
| [23] | Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69 Suppl 8184–193.
|
| [24] | Shi X, Zhang J, He Z, Shang Y, Xu D (2011) A sampling-based method for ranking protein structural models by integrating multiple scores and features. Curr Protein Pept Sci 12: 540–548.
|
| [25] | Qiu J, Sheffler W, Baker D, Noble WS (2008) Ranking predicted protein structures with support vector regression. Proteins 71: 1175–1182.
|
| [26] | He Z, Zhang J, Xu Y, Shang Y, Xu D (2011) Protein structural model selection based on protein-dependent scoring function. Statistics and Its Interface Volume 0.
|
| [27] | Zhang J, Zhang Y (2010) A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One 5: e15386.
|
| [28] | Zheng W, Liu X (2005) A protein structural alphabet and its substitution matrix CLESUM. Transactions on Computational Systems Biology II Volume 3680: 59–67.
|
| [29] | McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16: 404–405.
|
| [30] | Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577–2637.
|
| [31] | Cheng J, Randall AZ, Sweredoski MJ, Baldi P (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 33: W72–76.
|
| [32] | Faraggi E, Xue B, Zhou Y (2009) Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network. Proteins 74: 847–856.
|
| [33] | Gao X, Bu D, Xu J, Li M (2009) Improving consensus contact prediction via server correlation reduction. BMC Struct Biol 9: 28.
|
