Goto

Collaborating Authors

EU Denies Ready to Make Binding Brexit Tweaks

U.S. News

Responding to reports of comments made by the lawmakers, which suggested the EU would consider legally binding assurances on how the withdrawal agreement would operate, Selmayr tweeted: "On the EU side, nobody is considering this. Asked whether any assurance would help to get the Withdrawal Agreement through the Commons, the answers of MPs were inconclusive."


Genderqueer Massage Therapist Helps With Chest Binding Pain

U.S. News

Reed starts each class by sharing this story, and teaching students how to mitigate pain and prevent injuries of their own. They urge students to spend a few minutes a day going through self-massaging techniques. Reed demonstrates how to massage their diaphragm muscle tissue near the edge of the binder and how to roll a tennis ball against their trapezius muscle using a corner of a wall. In another technique, Reed lies down on a roller and extends their arms toward the floor, opening their chest.


An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem

AAAI Conferences

This is an investigation of methods for finding short motifs that only occur in a fraction of the input sequences. Unlike local search techniques that may not reach a global optimum, the method proposed here is guaranteed to produce the motifs with greatest z-scores.


Predicting the Geometry of Metal Binding Sites from Protein Sequence

Neural Information Processing Systems

Metal binding is important for the structural and functional characterization of proteins. Previous prediction efforts have only focused on bonding state, i.e. deciding which protein residues act as metal ligands in some binding site. Identifying the geometry of metal-binding sites, i.e. deciding which residues are jointly involved in the coordination of a metal ion is a new prediction problem that has been never attempted before from protein sequence alone. In this paper, we formulate it in the framework of learning with structured outputs. Our solution relies on the fact that, from a graph theoretical perspective, metal binding has the algebraic properties of a matroid, enabling the application of greedy algorithms for learning structured outputs.


DeepDTA: Deep Drug-Target Binding Affinity Prediction

arXiv.org Machine Learning

The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-ligand interactions assume a continuum of binding strength values, also called binding affinity and predicting this value still remains a challenge. The increase in the affinity data available in DT knowledge-bases allow the use of advanced learning techniques such as deep learning architectures in the prediction of binding affinities. In this study, we propose a deep-learning based model that uses only sequence information of both targets and drugs to predict DT interaction binding affinities. The few studies that focus on DT binding affinity prediction either use 3D structure of protein-ligand complexes or 2D features of compounds. One novel approach used in this work is the modeling of protein sequences and compound 1D representations with convolutional neural networks (CNNs). The results show that the proposed deep learning based model that uses the 1D representations of targets and drugs is an effective approach for drug target binding affinity prediction. The model in which a high-level representation of a drug is constructed via CNNs and Smith-Waterman similarity is used for proteins achieved the best Concordance Index (CI) performance, outperforming KronRLS, a state-of-the-art algorithm for DT binding affinity prediction, with statistical significance.