Volume 85, Issue 4, Pages 2119-2146 (October 2003) ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence  J.L. Klepeis, C.A. Floudas  Biophysical Journal  Volume 85, Issue 4, Pages 2119-2146 (October 2003) DOI: 10.1016/S0006-3495(03)74640-2 Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 1 Overall schematic of ASTRO-FOLD approach for three-dimensional structure prediction of proteins. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 2 Probability of α-helix formation for T59. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 3 Contact diagram for global optimum of strand contact formulation for protein Sm D3 (T59). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 4 Qualitative mapping of predicted β-strand to experimental structure of T59. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 5 Contact diagram for strand contact formulation with modified β-strand prediction for protein Sm D3 (T59). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 6 Comparison of predicted lowest energy tertiary structure (black) of T59 and experimentally determined structure (gray). All images generated with the RASMOL molecular visualization package (Sayle and Milner-White, 1995). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 7 Contact diagram for global optimum strand-to-strand prediction for T114. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 8 Qualitative mapping of predicted β-strand to experimental structure of T114. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 9 Comparison of predicted lowest energy tertiary structure (black) of T114 and experimentally determined structure (gray). All images generated with the RASMOL molecular visualization package (Sayle and Milner-White, 1995). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 10 Probability of α-helix formation for T170. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 11 Comparison of predictions for helix and β-strand locations with respect to the experimental observations. For each target, the top line represents the secondary structure content of the experimentally determined structure, whereas the second line identifies the subsequent prediction results. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 12 Contact map comparisons (clockwise from top left) for T130, T138, T160, and T150. The upper left triangle corresponds to interatomic distances calculated from the experimental structure, whereas the lower right triangle corresponds to those derived from the predicted structure. An upper distance cutoff of 30Å was used to emphasize small interatomic distances. The progression from small to large distances follows the dark to light shading. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 13 Average backbone RMSDs from experimental structure for helical (top) and β-strand (bottom) regions (length given by values on x-axis) of all CASP targets. Helix and strand locations defined as in experimental structures. Standard deviations are also provided. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 14 Average backbone RMSDs from experimental structure for loop regions (length given by values on x-axis) of all CASP targets. Loop locations defined as in experimental structures. Standard deviations are also provided. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 15 Smallest RMSDs for longest continuous segment between predicted and experimental structures of CASP targets. The RMS values are plotted versus the fraction of the total sequence represented by the longest continuous segments providing that RMS value. The top plot is for sequences with lengths <110 amino acids, whereas the bottom plot is for the remaining longer length sequences. Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 16 Comparison of predicted lowest energy tertiary structure (left) and experimentally determined structure (right) for T132 and T137 (top to bottom). All images generated with the RASMOL molecular visualization package (Sayle and Milner-White, 1995). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 17 Comparison of predicted lowest energy tertiary structure (left) and experimentally determined structure (right) for T139 and T170 (top to bottom). All images generated with the RASMOL molecular visualization package (Sayle and Milner-White, 1995). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 18 Comparison of predicted lowest energy tertiary structure (left) and experimentally determined structure (right) for T138 and T160 (top to bottom). All images generated with the RASMOL molecular visualization package (Sayle and Milner-White, 1995). Biophysical Journal 2003 85, 2119-2146DOI: (10.1016/S0006-3495(03)74640-2) Copyright © 2003 The Biophysical Society Terms and Conditions