Beyond the Black Box: Interactive Global Docking of Protein Complexes

Beyond the Black Box: Interactive Global Docking of Protein Complexes

Beyond the black box

As developers of SageMath, we show how open software facilitates corrections. “Commercial computer algebra systems are black boxes, and their algorithms are opaque to the users,” complained a trio ofmathematicianswhose “misfortunes” are detailed in a recent Notices article [2]. “We reported the bug on October 7, 2013...By June 2014, nothing had changed ...All we could do was wait.”

Beyond the Black Box Approach to Ethics!; Comment on “Expanded HTA: Enhancing Fairness and Legitimacy”

In the editorial published in this journal, Daniels and colleagues argue that his and Sabin’s accountability for reasonableness (A4R) framework should be used to handle ethical issues in the health technology assessment (HTA)-process, especially concerning fairness. In contrast to this suggestion, it is argued that such an approach risks suffering from the irrrelevance or insufficiency they war...

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

SUMMARY Protein-protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict str...

How to Go Beyond the Black-Box Simulation Barrier

The simulation paradigm is central to cryptography. A simulator is an algorithm that tries to simulate the interaction of the adversary with an honest party, without knowing the private input of this honest party. Almost all known simulators use the adversary’s algorithm as a black-box. We present the first constructions of non-black-box simulators. Using these new non-black-box techniques we o...