			Home About us Contact

Loop Closure (loop + closure)

Distribution by Scientific Domains

Chemistry	40%

Selected Abstracts

Automatic appearance-based loop detection from three-dimensional laser data using the normal distributions transform

JOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 11-12 2009
Martin Magnusson
We propose a new approach to appearance-based loop detection for mobile robots, using three-dimensional (3D) laser scans. Loop detection is an important problem in the simultaneous localization and mapping (SLAM) domain, and, because it can be seen as the problem of recognizing previously visited places, it is an example of the data association problem. Without a flat-floor assumption, two-dimensional laser-based approaches are bound to fail in many cases. Two of the problems with 3D approaches that we address in this paper are how to handle the greatly increased amount of data and how to efficiently obtain invariance to 3D rotations. We present a compact representation of 3D point clouds that is still discriminative enough to detect loop closures without false positives (i.e., detecting loop closure where there is none). A low false-positive rate is very important because wrong data association could have disastrous consequences in a SLAM algorithm. Our approach uses only the appearance of 3D point clouds to detect loops and requires no pose information. We exploit the normal distributions transform surface representation to create feature histograms based on surface orientation and smoothness. The surface shape histograms compress the input data by two to three orders of magnitude. Because of the high compression rate, the histograms can be matched efficiently to compare the appearance of two scans. Rotation invariance is achieved by aligning scans with respect to dominant surface orientations. We also propose to use expectation maximization to fit a gamma mixture model to the output similarity measures in order to automatically determine the threshold that separates scans at loop closures from nonoverlapping ones. We discuss the problem of determining ground truth in the context of loop detection and the difficulties in comparing the results of the few available methods based on range information. Furthermore, we present quantitative performance evaluations using three real-world data sets, one of which is highly self-similar, showing that the proposed method achieves high recall rates (percentage of correctly identified loop closures) at low false-positive rates in environments with different characteristics. © 2009 Wiley Periodicals, Inc. [source]

Low free energy cost of very long loop insertions in proteins

PROTEIN SCIENCE, Issue 2 2003
Michelle Scalley-Kim
Abstract Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded structure with amino- and carboxy-termini in close proximity. A loop entropy reduction screen based on this concept was used in an attempt to retrieve folded sequences from random sequence libraries. A library of long random sequences was inserted into a loop of the SH2 domain, displayed on the surface of M13 phage, and the inserted sequences that did not disrupt SH2 function were retrieved by panning using beads coated with a phosphotyrosine containing SH2 peptide ligand. Two sequences of a library of 2 × 108 sequences were isolated after multiple rounds of panning, and were found to have recovery levels similar to the wild-type SH2 domain and to be relatively intolerant to further mutation in PCR mutagenesis experiments. Surprisingly, although these inserted sequences exhibited little nonrandom structure, they do not significantly destabilize the host SH2 domain. Additional insertion variants recovered at lower levels in the panning experiments were also found to have a minimal effect on the stability and peptide-binding function of the SH2 domain. The additional level of selection present in the panning experiments is likely to involve in vivo folding and assembly, as there was a rough correlation between recovery levels in the phage-panning experiments and protein solubility. The finding that loop insertions of 60,80 amino acids have minimal effects on SH2 domain stability suggests that the free energy cost of inserting long loops may be considerably less than polymer theory estimates based on the entropic cost of loop closure, and, hence, that loop insertion may have provided an evolutionary route to multidomain protein structures. [source]

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009
P. Gayathri
Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The kcat values and Km values are (2.54 ± 0.19) × 105,min,1 and 0.39 ± 0.049,mM, respectively, for the wild type; (3.72 ± 0.28) × 103,min,1 and 2.18 ± 0.028,mM, respectively, for the F96S mutant; (1.11 ± 0.03) × 104,min,1 and 2.62 ± 0.042,mM, respectively, for the F96H mutant; and (1.48 ± 0.05) × 105,min,1 and 1.20 ± 0.056,mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM. [source]