MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

BACKGROUND: Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed. RESULTS: We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, C(α) only models, Alternative alignments, and Non-sequential alignments). The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here. CONCLUSIONS: MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective tool for automatically detecting non-trivial structural relationships of proteins, such as circular permutations and segment-swapping, many of which have been identified manually by human experts so far. The source code of MICAN is freely download-able at http://www.tbp.cse.nagoya-u.ac.jp/MICAN

Fine-To-Coarse Global Registration of RGB-D Scans

RGB-D scanning of indoor environments is important for many applications, including real estate, interior design, and virtual reality. However, it is still challenging to register RGB-D images from a hand-held camera over a long video sequence into a globally consistent 3D model. Current methods often can lose tracking or drift and thus fail to reconstruct salient structures in large environments (e.g., parallel walls in different rooms). To address this problem, we propose a "fine-to-coarse" global registration algorithm that leverages robust registrations at finer scales to seed detection and enforcement of new correspondence and structural constraints at coarser scales. To test global registration algorithms, we provide a benchmark with 10,401 manually-clicked point correspondences in 25 scenes from the SUN3D dataset. During experiments with this benchmark, we find that our fine-to-coarse algorithm registers long RGB-D sequences better than previous methods

Preserving Trustworthiness and Confidentiality for Online Multimedia

Technology advancements in areas of mobile computing, social networks, and cloud computing have rapidly changed the way we communicate and interact. The wide adoption of media-oriented mobile devices such as smartphones and tablets enables people to capture information in various media formats, and offers them a rich platform for media consumption. The proliferation of online services and social networks makes it possible to store personal multimedia collection online and share them with family and friends anytime anywhere. Considering the increasing impact of digital multimedia and the trend of cloud computing, this dissertation explores the problem of how to evaluate trustworthiness and preserve confidentiality of online multimedia data. The dissertation consists of two parts. The first part examines the problem of evaluating trustworthiness of multimedia data distributed online. Given the digital nature of multimedia data, editing and tampering of the multimedia content becomes very easy. Therefore, it is important to analyze and reveal the processing history of a multimedia document in order to evaluate its trustworthiness. We propose a new forensic technique called ``Forensic Hash", which draws synergy between two related research areas of image hashing and non-reference multimedia forensics. A forensic hash is a compact signature capturing important information from the original multimedia document to assist forensic analysis and reveal processing history of a multimedia document under question. Our proposed technique is shown to have the advantage of being compact and offering efficient and accurate analysis to forensic questions that cannot be easily answered by convention forensic techniques. The answers that we obtain from the forensic hash provide valuable information on the trustworthiness of online multimedia data. The second part of this dissertation addresses the confidentiality issue of multimedia data stored with online services. The emerging cloud computing paradigm makes it attractive to store private multimedia data online for easy access and sharing. However, the potential of cloud services cannot be fully reached unless the issue of how to preserve confidentiality of sensitive data stored in the cloud is addressed. In this dissertation, we explore techniques that enable confidentiality-preserving search of encrypted multimedia, which can play a critical role in secure online multimedia services. Techniques from image processing, information retrieval, and cryptography are jointly and strategically applied to allow efficient rank-ordered search over encrypted multimedia database and at the same time preserve data confidentiality against malicious intruders and service providers. We demonstrate high efficiency and accuracy of the proposed techniques and provide a quantitative comparative study with conventional techniques based on heavy-weight cryptography primitives

The LabelHash algorithm for substructure matching

Background: There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However, experimental protein function determination is expensive and very time-consuming. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Results: We present LabelHash, a novel algorithm for matching substructural motifs to large collections of protein structures. The algorithm consists of two phases. In the first phase the proteins are preprocessed in a fashion that allows for instant lookup of partial matches to any motif. In the second phase, partial matches for a given motif are expanded to complete matches. The general applicability of the algorithm is demonstrated with three different case studies. First, we show that we can accurately identify members of the enolase superfamily with a single motif. Next, we demonstrate how LabelHash can complement SOIPPA, an algorithm for motif identification and pairwise substructure alignment. Finally, a large collection of Catalytic Site Atlas motifs is used to benchmark the performance of the algorithm. LabelHash runs very efficiently in parallel; matching a motif against all proteins in the 95 % sequence identity filtered non-redundant Protein Data Bank typically takes no more than a few minutes. The LabelHash algorithm is available through a web server and as a suite of standalone programs a

Recurring side-chain triads in monomeric enzymatic structures

An algorithm was developed to exhaustively screen monomeric enzymatic structures for recurring 3-residue side-chain arrangements. The algorithm was used in the screening of two datasets: 100 enzymatic structures with a recurring 3-residue active site, and 100 enzymatic structures with a unique 3-residue active site. In each structure, the algorithm considered all distinct side-chain triads that can be compiled from the entire complement of residues in a single isolated chain. Increasing chain length demonstrated a logarithmic growth in the number of recurring triads. The distribution of total distances in recurring triads adhered to normality while the distribution of unique triad distances appeared negatively skewed. Analysis of variance indicated that the means of maximum and average total distances are significantly greater in unique triads than in recurring triads. Screening for recurring triads in synthetically generated alternative rotamer structures demonstrated an overall decrease in the percent of recurring triads, as compared to the natural structures

Rekonstruktion und skalierbare Detektion und Verfolgung von 3D Objekten

The task of detecting objects in images is essential for autonomous systems to categorize, comprehend and eventually navigate or manipulate its environment. Since many applications demand not only detection of objects but also the estimation of their exact poses, 3D CAD models can prove helpful since they provide means for feature extraction and hypothesis refinement. This work, therefore, explores two paths: firstly, we will look into methods to create richly-textured and geometrically accurate models of real-life objects. Using these reconstructions as a basis, we will investigate on how to improve in the domain of 3D object detection and pose estimation, focusing especially on scalability, i.e. the problem of dealing with multiple objects simultaneously.Objekterkennung in Bildern ist für ein autonomes System von entscheidender Bedeutung, um seine Umgebung zu kategorisieren, zu erfassen und schließlich zu navigieren oder zu manipulieren. Da viele Anwendungen nicht nur die Erkennung von Objekten, sondern auch die Schätzung ihrer exakten Positionen erfordern, können sich 3D-CAD-Modelle als hilfreich erweisen, da sie Mittel zur Merkmalsextraktion und Verfeinerung von Hypothesen bereitstellen. In dieser Arbeit werden daher zwei Wege untersucht: Erstens werden wir Methoden untersuchen, um strukturreiche und geometrisch genaue Modelle realer Objekte zu erstellen. Auf der Grundlage dieser Konstruktionen werden wir untersuchen, wie sich der Bereich der 3D-Objekterkennung und der Posenschätzung verbessern lässt, wobei insbesondere die Skalierbarkeit im Vordergrund steht, d.h. das Problem der gleichzeitigen Bearbeitung mehrerer Objekte