4,152 research outputs found
iPose: Instance-Aware 6D Pose Estimation of Partly Occluded Objects
We address the task of 6D pose estimation of known rigid objects from single
input images in scenarios where the objects are partly occluded. Recent
RGB-D-based methods are robust to moderate degrees of occlusion. For RGB
inputs, no previous method works well for partly occluded objects. Our main
contribution is to present the first deep learning-based system that estimates
accurate poses for partly occluded objects from RGB-D and RGB input. We achieve
this with a new instance-aware pipeline that decomposes 6D object pose
estimation into a sequence of simpler steps, where each step removes specific
aspects of the problem. The first step localizes all known objects in the image
using an instance segmentation network, and hence eliminates surrounding
clutter and occluders. The second step densely maps pixels to 3D object surface
positions, so called object coordinates, using an encoder-decoder network, and
hence eliminates object appearance. The third, and final, step predicts the 6D
pose using geometric optimization. We demonstrate that we significantly
outperform the state-of-the-art for pose estimation of partly occluded objects
for both RGB and RGB-D input
Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
The equilibrium free energy landscape of off-lattice model heteropolymers as
a function of an internal coordinate, namely the end-to-end distance, is
reconstructed from out-of-equilibrium steered molecular dynamics data. This
task is accomplished via two independent methods: by employing an extended
version of the Jarzynski equality (EJE) and the inherent structure (IS)
formalism. A comparison of the free energies estimated with these two schemes
with equilibrium results obtained via the umbrella sampling technique reveals a
good quantitative agreement among all the approaches in a range of temperatures
around the ``folding transition'' for the two examined sequences. In
particular, for the sequence with good foldability properties, the mechanically
induced structural transitions can be related to thermodynamical aspects of
folding. Moreover, for the same sequence the knowledge of the landscape profile
allows for a good estimation of the life times of the native configuration for
temperatures ranging from the folding to the collapse temperature. For the
random sequence, mechanical and thermal unfolding appear to follow different
paths along the landscape.Comment: Latex manuscript, 20 pages, 23 figures, submitted to Physical Review
Distances and classification of amino acids for different protein secondary structures
Window profiles of amino acids in protein sequences are taken as a
description of the amino acid environment. The relative entropy or
Kullback-Leibler distance derived from profiles is used as a measure of
dissimilarity for comparison of amino acids and secondary structure
conformations. Distance matrices of amino acid pairs at different conformations
are obtained, which display a non-negligible dependence of amino acid
similarity on conformations. Based on the conformation specific distances
clustering analysis for amino acids is conducted.Comment: 15 pages, 8 figure
Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
We present the results of a self-consistent, unified molecular dynamics study
of simple model heteropolymers in the continuum with emphasis on folding,
sequence design and the determination of the interaction parameters of the
effective potential between the amino acids from the knowledge of the native
states of the designed sequences.Comment: 8 pages, 3 Postscript figures, uses RevTeX. Submitted to Physical
Review Letter
DichroMatch: a website for similarity searching of circular dichroism spectra
Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk
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