Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems

A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains elusive. One of the reasons is that proteins are not acting alone, but are specifically interacting with other proteins and biomolecules, forming intricate interaction networks that are essential for the majority of cell processes and pathological conditions. Thus, characterizing such interaction networks is an important step in understanding how information flows from gene to phenotype. Indeed, structural characterization of protein–protein interactions at atomic resolution has many applications in biomedicine, from diagnosis and vaccine design, to drug discovery. However, despite the advances of experimental structural determination, the number of interactions for which there is available structural data is still very small. In this context, a complementary approach is computational modeling of protein interactions by docking, which is usually composed of two major phases: (i) sampling of the possible binding modes between the interacting molecules and (ii) scoring for the identification of the correct orientations. In addition, prediction of interface and hot-spot residues is very useful in order to guide and interpret mutagenesis experiments, as well as to understand functional and mechanistic aspects of the interaction. Computational docking is already being applied to specific biomedical problems within the context of personalized medicine, for instance, helping to interpret pathological mutations involved in protein–protein interactions, or providing modeled structural data for drug discovery targeting protein–protein interactions.Spanish Ministry of Economy grant number BIO2016-79960-R; D.B.B. is supported by a predoctoral fellowship from CONACyT; M.R. is supported by an FPI fellowship from the Severo Ochoa program. We are grateful to the Joint BSC-CRG-IRB Programme in Computational Biology.Peer ReviewedPostprint (author's final draft

Skeleton-Based Human Action Recognition with Global Context-Aware Attention LSTM Networks

Human action recognition in 3D skeleton sequences has attracted a lot of research attention. Recently, Long Short-Term Memory (LSTM) networks have shown promising performance in this task due to their strengths in modeling the dependencies and dynamics in sequential data. As not all skeletal joints are informative for action recognition, and the irrelevant joints often bring noise which can degrade the performance, we need to pay more attention to the informative ones. However, the original LSTM network does not have explicit attention ability. In this paper, we propose a new class of LSTM network, Global Context-Aware Attention LSTM (GCA-LSTM), for skeleton based action recognition. This network is capable of selectively focusing on the informative joints in each frame of each skeleton sequence by using a global context memory cell. To further improve the attention capability of our network, we also introduce a recurrent attention mechanism, with which the attention performance of the network can be enhanced progressively. Moreover, we propose a stepwise training scheme in order to train our network effectively. Our approach achieves state-of-the-art performance on five challenging benchmark datasets for skeleton based action recognition

NASA/NBS (National Aeronautics and Space Administration/National Bureau of Standards) standard reference model for telerobot control system architecture (NASREM)

The document describes the NASA Standard Reference Model (NASREM) Architecture for the Space Station Telerobot Control System. It defines the functional requirements and high level specifications of the control system for the NASA space Station document for the functional specification, and a guideline for the development of the control system architecture, of the 10C Flight Telerobot Servicer. The NASREM telerobot control system architecture defines a set of standard modules and interfaces which facilitates software design, development, validation, and test, and make possible the integration of telerobotics software from a wide variety of sources. Standard interfaces also provide the software hooks necessary to incrementally upgrade future Flight Telerobot Systems as new capabilities develop in computer science, robotics, and autonomous system control

Fast filtering and animation of large dynamic networks

Detecting and visualizing what are the most relevant changes in an evolving network is an open challenge in several domains. We present a fast algorithm that filters subsets of the strongest nodes and edges representing an evolving weighted graph and visualize it by either creating a movie, or by streaming it to an interactive network visualization tool. The algorithm is an approximation of exponential sliding time-window that scales linearly with the number of interactions. We compare the algorithm against rectangular and exponential sliding time-window methods. Our network filtering algorithm: i) captures persistent trends in the structure of dynamic weighted networks, ii) smoothens transitions between the snapshots of dynamic network, and iii) uses limited memory and processor time. The algorithm is publicly available as open-source software.Comment: 6 figures, 2 table