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Background Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don’t account for halogen bonding in their scoring functions and are not able to utilize this new approach. In this study a new and improved halogen bonding scoring function (XBSF) is presented along with its implementation in the AutoDock Vina molecular docking software. This new improved program is termed as AutoDock VinaXB, where XB stands for the halogen bonding parameters that were added. Results XBSF scoring function is derived based on the X···A distance and C–X···A angle of interacting atoms. The distance term was further corrected to account for the polar flattening effect of halogens. A total of 106 protein-halogenated ligand complexes were tested and compared in terms of binding affinity and docking poses using Vina and VinaXB. VinaXB performed superior to Vina in the majority of instances. VinaXB was closer to native pose both above and below 2 Å deviation categories almost twice as frequently as Vina. Conclusions Implementation of XBSF into AutoDock Vina has been shown to improve the accuracy of the docking result with regards to halogenated ligands. AutoDock VinaXB addresses the issues of halogen bonds that were previously being scored unfavorably due to repulsion factors, thus effectively lowering the output RMSD values.

This Article reports the results of a survey of a diverse group of forty-two federal appellate judges concerning their approaches to statutory interpretation. The study reveals important differences between their approaches and the approach that the Supreme Court purports to take. It also helps to substantiate the irrelevance of the enduring, but nowboring, textualism-versus-purposivism debate. None of the judges we interviewed was willing to associate himself or herself with “textualism” without qualification. All consult legislative history. Most eschew dictionaries. All utilize at least some canons of construction, but for reasons that range from “window dressing,” to the use of canons to assist in opinion writing, to a view that they are useful decision tools. Most of the judges we interviewed are not fans of Chevron, except for the judges on the D.C. Circuit, which hears the bulk of Chevron cases. Some of the judges interviewed believe that understanding Congress is important to a judge’s work, while others do not see how judges can use such understanding to decide cases. Most express doubt that the Supreme Court’s interpretive methodology binds the lower courts. The younger judges, who attended law school and practiced during the ascendance of textualism, are generally more formalist and accepting of the canons of construction, regardless of political affiliation. The older judges are less focused on canons, take a broader view of their delegated authority, and appear to grapple more with questions of judicial legitimacy. The approach that emerged most clearly from our interviews might be described as intentional eclecticism. Most of the judges we spoke to are willing to consider many different kinds of argument and evidence, and defend that approach as the only democratically legitimate one. Yet at the same time many observe a gap between how they actually decide cases and how they write opinions, a gap they attribute to the disconnect between the expectations of the public and the realities of judicial decisionmaking.

Judicial self-restraint, once a rallying cry for judges and law professors, has fallen on evil days. It is rarely invoked or advocated. This Essay traces the rise and fall of its best-known variant—restraint in invalidating legislative action as unconstitutional—as advocated by the \"School of Thayer,\" consisting of James Bradley Thayer and the influential judges and law professors who claimed to be his followers. The Essay argues, among other things, that both the strength and the weakness of the School was an acknowledged absence of a theory of how to decide a constitutional case. The rise of constitutional theory created an unbearable tension between Thayer's claim that judges should uphold a statute unless its invalidity was clear beyond doubt (as it would very rarely be), and constitutional theories that claimed to dispel doubt and yield certifiably right answers in all cases.

This Article reports the results of a survey of a diverse group of forty-two federal appellate judges concerning their approaches to statutory interpretation. The study reveals important differences between their approaches and the approach that the Supreme Court purports to take. It also helps to substantiate the irrelevance of the enduring, but nowboring, textualism-versus-purposivism debate. None of the judges we interviewed was willing to associate himself or herself with \"textualism\" without qualification. All consult legislative history. Most eschew dictionaries. All utilize at least some canons of construction, but for reasons that range from \"window dressing,\" to the use of canons to assist in opinion writing, to a view that they are useful decision tools. Most of the judges we interviewed are not fans of Chevron, except for the judges on the D.C. Circuit, which hears the bulk of Chevron cases. Some of the judges interviewed believe that understanding Congress is important to a judge's work, while others do not see how judges can use such understanding to decide cases. Most express doubt that the Supreme Court's interpretive methodology binds the lower courts. The younger judges, who attended law school and practiced during the ascendance of textualism, are generally more formalist and accepting of the canons of construction, regardless of political affiliation. The older judges are less focused on canons, take a broader view of their delegated authority, and appear to grapple more with questions of judicial legitimacy. The approach that emerged most clearly from our interviews might be described as intentional eclecticism. Most of the judges we spoke to are willing to consider many different kinds of argument and evidence, and defend that approach as the only democratically legitimate one. Yet at the same time many observe a gap between how they actually decide cases and how they write opinions, a gap they attribute to the disconnect between the expectations of the public and the realities of judicial decisionmaking.

To increase situational awareness and support evidence-based policymaking, we formulated a mathematical model for coronavirus disease transmission within a regional population. This compartmental model accounts for quarantine, self-isolation, social distancing, a nonexponentially distributed incubation period, asymptomatic persons, and mild and severe forms of symptomatic disease. We used Bayesian inference to calibrate region-specific models for consistency with daily reports of confirmed cases in the 15 most populous metropolitan statistical areas in the United States. We also quantified uncertainty in parameter estimates and forecasts. This online learning approach enables early identification of new trends despite considerable variability in case reporting.

In systems biology, qualitative data are often generated, but rarely used to parameterize models. We demonstrate an approach in which qualitative and quantitative data can be combined for parameter identification. In this approach, qualitative data are converted into inequality constraints imposed on the outputs of the model. These inequalities are used along with quantitative data points to construct a single scalar objective function that accounts for both datasets. To illustrate the approach, we estimate parameters for a simple model describing Raf activation. We then apply the technique to a more elaborate model characterizing cell cycle regulation in yeast. We incorporate both quantitative time courses (561 data points) and qualitative phenotypes of 119 mutant yeast strains (1647 inequalities) to perform automated identification of 153 model parameters. We quantify parameter uncertainty using a profile likelihood approach. Our results indicate the value of combining qualitative and quantitative data to parameterize systems biology models. Much of the data generated in biology is qualitative, but exploiting such data to inform models of biological systems remains a challenge. Here, the authors demonstrate an approach that allows use of both quantitative and qualitative data for parameterising dynamical models.

Argues that the United States Supreme Court is generally a political organ when it is deciding constitutional cases & discusses the implications. Discussion opens with a look at some statistics that shed light on the tendency of the Court to behave legislatively & the perception of the Court as an increasingly constitutional court. \"Aggressive\" & \"modest\" forms of political judgment are distinguished before laying out alternatives to the political conception of the Supreme Court: as expert administrator, institutionally constrained, moral vanguard, & cosmopolitan. Consideration reveals the first two as descriptively inaccurate & the latter two as political versions masquerading as something Drawing on recent cases, the potential for the Court to be a \"modest\" & pragmatic decision maker is demonstrated. J. Zendejas

This title was first published in 2001. Transcending the divide between the English pragmatic tradition and the circularity of American policy-based theory, Michael Whincop and Mary Keyes argue that the laws governing multistage conflicts can minimize the social costs of litigation, increase the extent of co-ordination, facilitate private ordering and limit regulatory monopolies and cross-border spillovers. Pragmatic in outlook and economic in methodology, they pursue these themes across a broad range of doctrinal issues and offer valuable links to parallel analyses in domestic contexts.

The aged wife, in my appropriation of Tennyson, is not the mother of my children but the federal judiciary, much in need of improvement, and the subject of this Essay is what academic research of a particular type can do to help improve the federal judiciary.

The traditional focus of economic analysis of intellectual property has been on reconciling incentives for producing such property with concerns about restricting access to it by granting exclusive rights in intellectual goods - that is, by propertizing them - thus enabling the owner to charge a price for access that exceeds marginal cost. With the rise of the law and economics movement, the focus of economic analysis of intellectual property has begun to shift to more concrete and manageable issues concerning the structure and texture of the complicated pattern of common law and statutory doctrines, legal institutions and business practices relating to intellectual property. Among the issues discussed in this paper are the length of protection for intellectual property, the rules that allow considerable copying of intellectual property without permission of the originator, the rules governing derivative works, and alternative methods of providing incentives for the creation of intellectual property.