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Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein ... Figure 1. Workflow of the HawkDock.

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Presentation on theme: "Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein ... Figure 1. Workflow of the HawkDock."— Presentation transcript:

1 Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein ... Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein structures; (ii) structural prediction of protein–protein complex by using the global docking algorithm implemented in ATTRACT and the HawkRank scoring function; (iii) identification of the key residues by MM/GBSA. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz397, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Figure 2. Data input in the HawkDock server
Figure 2. Data input in the HawkDock server. (A) A HawkDock job needs: (1) optional job name and address, (2) PDB ... Figure 2. Data input in the HawkDock server. (A) A HawkDock job needs: (1) optional job name and address, (2) PDB files or PDB IDs, (3) optional distance restraints, (4) optional MM/GBSA re-scoring, (5) the ‘submit’ button and (6) the log of the HawkDock job. (B) A MM/GBSA job needs: (1) optional job name and address, (2) PDB file or PDB ID, (3) the chain IDs of receptor and ligand, (4) the ‘submit’ button and (5) the log of the MM/GBSA job. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz397, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Figure 3. The result pages of HawkDock and MM/GBSA
Figure 3. The result pages of HawkDock and MM/GBSA. (A) At the top left of the page is (1) the job name, and under it ... Figure 3. The result pages of HawkDock and MM/GBSA. (A) At the top left of the page is (1) the job name, and under it are (2) the files for downloading. (3) A summary of the docking scores for the top 10 models is presented on the left bottom. (4) The top 10 models can be viewed in 3Dmol.js with (5) the optional buttons to control which model to display. (6) The table summarizes the submission and results of MM/GBSA and (7) the brief instructions are shown on the bottom. (B) At the top of page is (1) the job name, and under it is (2) the value of the binding free energy and (3) the files for downloading. The per-residue free energy contributions ordered from largest to smallest for (4) receptor and (5) ligand are displayed in the table, (6) through which the users can choose which residue to display in 3Dmol.js. (7) The brief instructions are also displayed on the bottom. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz397, The content of this slide may be subject to copyright: please see the slide notes for details.

4 Figure 4. (A) The success rates from top 10 to top 1000 and top 1 to top 10 of HawkDock, ATTRACT, and ZDOCK 3.0.2, and ... Figure 4. (A) The success rates from top 10 to top 1000 and top 1 to top 10 of HawkDock, ATTRACT, and ZDOCK 3.0.2, and (B) the success rates of the key residues predicted by MM/GBSA. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz397, The content of this slide may be subject to copyright: please see the slide notes for details.

5 Figure 5. The structural alignment of the crystal structure (PDB ID: 3D5S) colored yellow and the theoretical model ... Figure 5. The structural alignment of the crystal structure (PDB ID: 3D5S) colored yellow and the theoretical model predicted by HawkDock (colored green). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz397, The content of this slide may be subject to copyright: please see the slide notes for details.

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