226 research outputs found
A bibliometric analysis of the Journal of Molecular Graphics and Modelling
This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported
Semi-Supervised Object Detection in the Open World
Existing approaches for semi-supervised object detection assume a fixed set
of classes present in training and unlabeled datasets, i.e., in-distribution
(ID) data. The performance of these techniques significantly degrades when
these techniques are deployed in the open-world, due to the fact that the
unlabeled and test data may contain objects that were not seen during training,
i.e., out-of-distribution (OOD) data. The two key questions that we explore in
this paper are: can we detect these OOD samples and if so, can we learn from
them? With these considerations in mind, we propose the Open World
Semi-supervised Detection framework (OWSSD) that effectively detects OOD data
along with a semi-supervised learning pipeline that learns from both ID and OOD
data. We introduce an ensemble based OOD detector consisting of lightweight
auto-encoder networks trained only on ID data. Through extensive evalulation,
we demonstrate that our method performs competitively against state-of-the-art
OOD detection algorithms and also significantly boosts the semi-supervised
learning performance in open-world scenarios
EigenFold: Generative Protein Structure Prediction with Diffusion Models
Protein structure prediction has reached revolutionary levels of accuracy on
single structures, yet distributional modeling paradigms are needed to capture
the conformational ensembles and flexibility that underlie biological function.
Towards this goal, we develop EigenFold, a diffusion generative modeling
framework for sampling a distribution of structures from a given protein
sequence. We define a diffusion process that models the structure as a system
of harmonic oscillators and which naturally induces a cascading-resolution
generative process along the eigenmodes of the system. On recent CAMEO targets,
EigenFold achieves a median TMScore of 0.84, while providing a more
comprehensive picture of model uncertainty via the ensemble of sampled
structures relative to existing methods. We then assess EigenFold's ability to
model and predict conformational heterogeneity for fold-switching proteins and
ligand-induced conformational change. Code is available at
https://github.com/bjing2016/EigenFold.Comment: ICLR MLDD workshop 202
Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity.
MYCBP2 is a ubiquitin (Ub) E3 ligase (E3) that is essential for neurodevelopment and regulates axon maintenance. MYCBP2 transfers Ub to nonlysine substrates via a newly discovered RING-Cys-Relay (RCR) mechanism, where Ub is relayed from an upstream cysteine to a downstream substrate esterification site. The molecular bases for E2-E3 Ub transfer and Ub relay are unknown. Whether these activities are linked to the neural phenotypes is also unclear. We describe the crystal structure of a covalently trapped E2~Ub:MYCBP2 transfer intermediate revealing key structural rearrangements upon E2-E3 Ub transfer and Ub relay. Our data suggest that transfer to the dynamic upstream cysteine, whilst mitigating lysine activity, requires a closed-like E2~Ub conjugate with tempered reactivity, and Ub relay is facilitated by a helix-coil transition. Furthermore, neurodevelopmental defects and delayed injury-induced degeneration in RCR-defective knock-in mice suggest its requirement, and that of substrate esterification activity, for normal neural development and programmed axon degeneration
2021-2022 New Friends Dreams and Directions
https://spiral.lynn.edu/foc-events/1038/thumbnail.jp
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