Docking accuracy enhanced by QM-derived protein charges

<p>Effects of protein polari sation on docking accuracy were investigated using molecular docking programme AutoDock 4 in which topology-specific empirical Gasteiger charges were replaced with Polarised protein-specific charges (PPC) to represent quantum mechanics- polarised protein. Docking was successfully conducted for 50 diverse protein–ligand complexes. The docking with PPC charges shows a decrease in the root-mean-square deviation (RMSD) values of ligands compared to those from the docking with Gasteiger charges. Ligand binding orientations and their key interactions such as hydrogen bonding interactions in X-ray structures were substantially reproduced in complexes docked using PPC scheme with 98% of the RMSDs of the best docking poses less than 2 Å compared to 74% in the docking with Gasteiger charges. Considerable improvements in docking accuracy were observed by simply altering the atomic partial charges in the scoring function, which reflects the importance of protein polarisation in molecular docking. Further research can be carried out to (1) include polarisation of both ligands and proteins to account for polarisation effects within protein and between protein and ligand, and (2) develop a PPC-based scoring function to increase the docking accuracies for protein–ligand complexes from a larger variety of protein families.</p

Unexpected Odd–Even Oscillation in the Enhanced Chemical Activities of the Ru_<i>n</i> (<i>n</i> = 2–14) Nanoclusters for H₂O Splitting

Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. In general, the more energetically stable the nanocluster, the weaker the reagent reacts with it; however, to date, it is still open whether all reactions are subject to such a fundamental constraint. Here, using first-principles calculations within density functional theory in consideration of van der Waals corrections and Gaussian 09 program, we investigate the energetic and kinetic properties of water molecules adsorption on small Ru_<i>n</i> (<i>n</i> = 2–14) clusters. It is found that almost all of the studied Ru_<i>n</i> clusters possess superior activities toward H₂O adsorption and dissociation, due to the enlarged desorption energies and reduced dissociation barriers when compared with the bulk Ru(0001) counterpart. More interestingly, though the stabilities of Ru_<i>n</i> clusters exhibit significant odd–even oscillation behavior, i.e., the even-numbered nanoclusters are distinctly more stable than their neighboring odd-numbered cases, the H₂O molecule adsorption on the even-numbered Ru_<i>n</i> clusters (such as <i>n</i> = 4, 6, 8, 10) leads to larger adsorption energies. We reveal that such intriguing activity can be explicated by a geometric effect, namely, the lowly coordinated atoms contribute the lowest-unoccupied molecular orbital protruding out of the cluster to capture the lone-pair electrons from H₂O molecule and determine the size-dependent chemical activities. These findings shed new insight into highly efficient and economic nanocatalysts design for the field of water splitting

Principle of crack length extraction.

China is gradually transitioning from the "tunnel construction exploration era" to the "tunnel high-quality construction and operation era", and the maintenance demand of highway tunnels has increased sharply. Therefore, there is an urgent need for an evaluation method to evaluate the service reliability of highway tunnels, so as to provide reference for tunnel maintenance personnel to carry out maintenance work. Taking highway tunnels as the research object, this paper extracts three parameters, including length, maximum width and fractal dimension, from the binary image of highway tunnel lining cracks. The standard for dividing the length of the highway tunnel section is 500m as the tunnel section, and a section disease sample space including multiple highway tunnels is constructed. The EM clustering algorithm was used to determine the number of graded grades of disease, and the relative Euclidean distance was used as the evaluation index to divide the safety grade of the tunnel into five grades: normal, degraded, inferior, deteriorated and hazardous. The partial least squares method is used to establish the lining service reliability evaluation formula and verify the residual of each sample point in the sample space. The smaller the average value of the residual, the better fitting effect of the established evaluation formula. The service reliability evaluation method proposed in this paper is applied to engineering practice and compared with the expert scoring method and the national standard method, which proves that the evaluation method in this paper has the advantages of strong visibility, simple evaluation method, and is conducive to engineering practice.</div

S1 Data -

China is gradually transitioning from the "tunnel construction exploration era" to the "tunnel high-quality construction and operation era", and the maintenance demand of highway tunnels has increased sharply. Therefore, there is an urgent need for an evaluation method to evaluate the service reliability of highway tunnels, so as to provide reference for tunnel maintenance personnel to carry out maintenance work. Taking highway tunnels as the research object, this paper extracts three parameters, including length, maximum width and fractal dimension, from the binary image of highway tunnel lining cracks. The standard for dividing the length of the highway tunnel section is 500m as the tunnel section, and a section disease sample space including multiple highway tunnels is constructed. The EM clustering algorithm was used to determine the number of graded grades of disease, and the relative Euclidean distance was used as the evaluation index to divide the safety grade of the tunnel into five grades: normal, degraded, inferior, deteriorated and hazardous. The partial least squares method is used to establish the lining service reliability evaluation formula and verify the residual of each sample point in the sample space. The smaller the average value of the residual, the better fitting effect of the established evaluation formula. The service reliability evaluation method proposed in this paper is applied to engineering practice and compared with the expert scoring method and the national standard method, which proves that the evaluation method in this paper has the advantages of strong visibility, simple evaluation method, and is conducive to engineering practice.</div

Calculation of fractal dimension of fracture with different cracks.

(a)FW = 1.1757, (b) FW = 1.1922, (c) FW = 1.2496, (d) FW = 1.3057.</p

Specific scores of expert scoring method.

China is gradually transitioning from the "tunnel construction exploration era" to the "tunnel high-quality construction and operation era", and the maintenance demand of highway tunnels has increased sharply. Therefore, there is an urgent need for an evaluation method to evaluate the service reliability of highway tunnels, so as to provide reference for tunnel maintenance personnel to carry out maintenance work. Taking highway tunnels as the research object, this paper extracts three parameters, including length, maximum width and fractal dimension, from the binary image of highway tunnel lining cracks. The standard for dividing the length of the highway tunnel section is 500m as the tunnel section, and a section disease sample space including multiple highway tunnels is constructed. The EM clustering algorithm was used to determine the number of graded grades of disease, and the relative Euclidean distance was used as the evaluation index to divide the safety grade of the tunnel into five grades: normal, degraded, inferior, deteriorated and hazardous. The partial least squares method is used to establish the lining service reliability evaluation formula and verify the residual of each sample point in the sample space. The smaller the average value of the residual, the better fitting effect of the established evaluation formula. The service reliability evaluation method proposed in this paper is applied to engineering practice and compared with the expert scoring method and the national standard method, which proves that the evaluation method in this paper has the advantages of strong visibility, simple evaluation method, and is conducive to engineering practice.</div

Calculation of various indicators of <i>HSR</i>.

China is gradually transitioning from the "tunnel construction exploration era" to the "tunnel high-quality construction and operation era", and the maintenance demand of highway tunnels has increased sharply. Therefore, there is an urgent need for an evaluation method to evaluate the service reliability of highway tunnels, so as to provide reference for tunnel maintenance personnel to carry out maintenance work. Taking highway tunnels as the research object, this paper extracts three parameters, including length, maximum width and fractal dimension, from the binary image of highway tunnel lining cracks. The standard for dividing the length of the highway tunnel section is 500m as the tunnel section, and a section disease sample space including multiple highway tunnels is constructed. The EM clustering algorithm was used to determine the number of graded grades of disease, and the relative Euclidean distance was used as the evaluation index to divide the safety grade of the tunnel into five grades: normal, degraded, inferior, deteriorated and hazardous. The partial least squares method is used to establish the lining service reliability evaluation formula and verify the residual of each sample point in the sample space. The smaller the average value of the residual, the better fitting effect of the established evaluation formula. The service reliability evaluation method proposed in this paper is applied to engineering practice and compared with the expert scoring method and the national standard method, which proves that the evaluation method in this paper has the advantages of strong visibility, simple evaluation method, and is conducive to engineering practice.</div

Sample space silhouette values when the number of grading is 5.

Sample space silhouette values when the number of grading is 5.</p

Subimage division of cracks.

China is gradually transitioning from the "tunnel construction exploration era" to the "tunnel high-quality construction and operation era", and the maintenance demand of highway tunnels has increased sharply. Therefore, there is an urgent need for an evaluation method to evaluate the service reliability of highway tunnels, so as to provide reference for tunnel maintenance personnel to carry out maintenance work. Taking highway tunnels as the research object, this paper extracts three parameters, including length, maximum width and fractal dimension, from the binary image of highway tunnel lining cracks. The standard for dividing the length of the highway tunnel section is 500m as the tunnel section, and a section disease sample space including multiple highway tunnels is constructed. The EM clustering algorithm was used to determine the number of graded grades of disease, and the relative Euclidean distance was used as the evaluation index to divide the safety grade of the tunnel into five grades: normal, degraded, inferior, deteriorated and hazardous. The partial least squares method is used to establish the lining service reliability evaluation formula and verify the residual of each sample point in the sample space. The smaller the average value of the residual, the better fitting effect of the established evaluation formula. The service reliability evaluation method proposed in this paper is applied to engineering practice and compared with the expert scoring method and the national standard method, which proves that the evaluation method in this paper has the advantages of strong visibility, simple evaluation method, and is conducive to engineering practice.</div

Disease sample space of section tunnels.

China is gradually transitioning from the "tunnel construction exploration era" to the "tunnel high-quality construction and operation era", and the maintenance demand of highway tunnels has increased sharply. Therefore, there is an urgent need for an evaluation method to evaluate the service reliability of highway tunnels, so as to provide reference for tunnel maintenance personnel to carry out maintenance work. Taking highway tunnels as the research object, this paper extracts three parameters, including length, maximum width and fractal dimension, from the binary image of highway tunnel lining cracks. The standard for dividing the length of the highway tunnel section is 500m as the tunnel section, and a section disease sample space including multiple highway tunnels is constructed. The EM clustering algorithm was used to determine the number of graded grades of disease, and the relative Euclidean distance was used as the evaluation index to divide the safety grade of the tunnel into five grades: normal, degraded, inferior, deteriorated and hazardous. The partial least squares method is used to establish the lining service reliability evaluation formula and verify the residual of each sample point in the sample space. The smaller the average value of the residual, the better fitting effect of the established evaluation formula. The service reliability evaluation method proposed in this paper is applied to engineering practice and compared with the expert scoring method and the national standard method, which proves that the evaluation method in this paper has the advantages of strong visibility, simple evaluation method, and is conducive to engineering practice.</div