Small molecule drugs are rarely selective enough to interact solely with their designated targets. Unintended "off-target" interactions often lead to side effects, but also serendipitously lead to new therapeutic uses. Identification of the off-targets of a compound is therefore of significant value to the evaluation of its developmental potential. In computational biology, the strategy of "reverse docking" has been introduced to predict the targets of a compound, which uses a compound to virtually screen a library of proteins, reversing the bait and prey in "normal" docking screenings. The present study shows that, in reverse docking, additional optimization of the scoring function may help to improve the target prediction accuracy. In a case study with the Glide scores, we found that only 57% of the ligand-protein relationships could be correctly identified in a library of 58 complexes whose crystal binding conformations were all able to be accurately reproduced. This was likely a result of the constant over- or under-estimation of the scores for specific proteins. In other words, there were interprotein noises in the Glide scores. Introducing a correction term based on protein characteristics improved the target-prediction accuracy by 27% (57-72%). It is our hope that this focused discussion on the Glide scores would invite further efforts to characterize and normalize this type of interprotein noises in all docking scores, so that better target prediction accuracy can be achieved with the strategy of reverse docking.
This work introduces the support vector rank regression (SVRR) algorithm for the optimization of molecular docking scores. Seven original docking scores reported by two docking software were integrated by the SVRR algorithm. The resulting SVRR scores showed an average of 12.1% improvement (59.5-66.7%) in binding conformation prediction tests to rank the correctly computed conformation in the first place, along with 16.7% RMSD improvement (2.5414 vs. 2.1162 Å) for the top ranked conformations. In compound library screening (LS) tests, an average of 46.3% improvement (18.2-26.6%) was also observed to rank the correct ligand in the first place. Furthermore, it was shown that SVRR scores trained with different example datasets, using different training strategies, all exhibited exceedingly consistent accuracies, suggesting that the SVRR algorithm is highly robust and generalizable. In contrast, using the same training datasets, traditional support vector classification and regression algorithms failed to improve comparably the accuracy of LS and conformation prediction. These results suggested that, with additional features to indicate the comparative fitness between computed binding conformations, the SVRR algorithm holds the potential to create a new category of more accurate integrative docking scores.
Background and Objective: Although depression is one of the most common non-motor symptoms in essential tremor (ET), its pathogenesis and diagnosis biomarker are still unknown. Recently, machine learning multivariate pattern analysis (MVPA) combined with connectivity mapping of resting-state fMRI has provided a promising way to identify patients with depressed ET at the individual level and help to reveal the brain network pathogenesis of depression in patients with ET.Methods: Based on global brain connectivity (GBC) mapping from 41 depressed ET, 49 non-depressed ET, 45 primary depression, and 43 healthy controls (HCs), multiclass Gaussian process classification (GPC) and binary support vector machine (SVM) algorithms were used to identify patients with depressed ET from non-depressed ET, primary depression, and HCs, and the accuracy and permutation tests were used to assess the classification performance.Results: While the total accuracy (40.45%) of four-class GPC was poor, the four-class GPC could discriminate depressed ET from non-depressed ET, primary depression, and HCs with a sensitivity of 70.73% (P < 0.001). At the same time, the sensitivity of using binary SVM to discriminate depressed ET from non-depressed ET, primary depression, and HCs was 73.17, 80.49, and 75.61%, respectively (P < 0.001). The significant discriminative features were mainly located in cerebellar-motor-prefrontal cortex circuits (P < 0.001), and a further correlation analysis showed that the GBC values of significant discriminative features in the right middle prefrontal gyrus, bilateral cerebellum VI, and Crus 1 were correlated with clinical depression severity in patients with depressed ET.Conclusion: Our findings demonstrated that GBC mapping combined with machine learning MVPA could be used to identify patients with depressed ET, and the GBC changes in cerebellar-prefrontal cortex circuits not only posed as the significant discriminative features but also helped to understand the network pathogenesis underlying depression in patients with ET.
BackgroundAlthough depression is one of the most common neuropsychiatric symptoms in essential tremor (ET), the diagnosis biomarker and intrinsic brain activity remain unclear. We aimed to combine multivariate pattern analysis (MVPA) with local brain functional connectivity to identify depressed ET.MethodsBased on individual voxel-level local brain functional connectivity (regional homogeneity, ReHo) mapping from 41 depressed ET, 43 non-depressed ET, and 45 healthy controls (HCs), the binary support vector machine (BSVM) and multiclass Gaussian Process Classification (MGPC) algorithms were used to identify depressed ET patients from non-depressed ET and HCs, the accuracy and permutations test were used to assess the classification performance.ResultsThe MGPC algorithm was able to classify the three groups (depressed ET, non-depressed ET, and HCs) with a total accuracy of 84.5%. The BSVM algorithm achieved a better classification performance with total accuracy of 90.7, 88.64, and 90.48% for depressed ET vs. HCs, non-depressed ET vs. HCs, and depressed ET vs. non-depressed ET, and the sensitivity for them at 80.49, 76.64, and 80.49%, respectively. The significant discriminative features of depressed ET vs. HCs were primarily located in the cerebellar-motor-prefrontal gyrus-anterior cingulate cortex pathway, and for depressed ET vs. non-depressed ET located in the cerebellar-prefrontal gyrus-anterior cingulate cortex circuits. The partial correlation showed that the ReHo values in the bilateral middle prefrontal gyrus (positive) and the bilateral cerebellum XI (negative) were significantly correlated with clinical depression severity.ConclusionOur findings suggested that combined individual ReHo maps with MVPA not only could be used to identify depressed ET but also help to reveal the intrinsic brain activity changes and further act as the potential diagnosis biomarker in depressed ET patients.
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