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A Bioinformatics Approach to 3D Shape Matching [chapter]

Manuele Bicego, Stefano Danese, Simone Melzi, Umberto Castellani
2015 Lecture Notes in Computer Science  
In this paper we exploit the effectiveness of bioinformatics tools to deal with 3D shape matching.  ...  The key idea is to transform the shape into a biological sequence and take advantage of bioinformatics tools for sequence alignment to improve shape matching.  ...  The key idea consists of encoding the 3D shape as a biological sequence and employing tailored bioinformatics tools to perform the matching.  ... 
doi:10.1007/978-3-319-16220-1_22 fatcat:assd7ottxjad5h46kwlgmdvlga

Protein Data Representation: A Survey

Ahmed S.Fadel, Mohamed Belal, Mostafa-Sami M. Mostafa
2012 International Journal of Computer Applications  
Hence, it could be a basic reference for research that is aiming to develop applications in the field of bioinformatics.  ...  One of the critical issues in bioinformatics is the data structure used for representing the protein data; this representation is a base for the operations applied such as sequence alignment, structure  ...  Protein 3D structure can be treated as a geometric shape.  ... 
doi:10.5120/8936-3075 fatcat:qcdrherrwfa6zpl7qtj7sncaky

A web-based three-dimensional protein retrieval system by matching visual similarity

J.-S. Yeh, D.-Y. Chen, B.-Y. Chen, M. Ouhyoung
2005 Bioinformatics  
In this system, we use a visual-based matching method to compare the protein structure from multiple viewpoints. It takes less than three seconds for each query with 90% accuracy on an average.  ...  A web-based three-dimensional (3D) protein retrieval system is available for protein structure data including all PDB and FSSP dataset.  ...  Shape histogram (Ankerst et al., 1999) is used to compare the 3D structure of the surface of proteins.  ... 
doi:10.1093/bioinformatics/bti458 pmid:15840701 fatcat:mio4b7shnfhdnbllwgdcfqxsue

Food volume computation for self dietary assessment applications

J. Dehais, S. Shevchik, P. Diem, S. G. Mougiakakou
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
A 3D model of the served meal is reconstructed using the acquired images and the volume is computed from the shape.  ...  The paper presents a computational system for volume estimation based on the processing of two meal images.  ...  These methods aim to align 3D shape primitives to the edges of the food captured by a photograph.  ... 
doi:10.1109/bibe.2013.6701615 dblp:conf/bibe/DehaisSDM13 fatcat:thxnv7mhkzaa3ip7oljotq65ue

A 3D pattern matching algorithm for DNA sequences

J. Herisson, G. Payen, R. Gherbi
2007 Bioinformatics  
The aim of this work is to enhance conventional pattern matching analyses with 3D-augmented criteria.  ...  By using 3D conformation models, one is able to construct a 3D trajectory of a naked DNA molecule.  ...  Such a 3D pattern tool offers a new way to integrate geometrical criteria into bioinformatics analyses. It leads to an improved or a complementary result for pattern matching.  ... 
doi:10.1093/bioinformatics/btl669 pmid:17237044 fatcat:4yckrpt4srcebjlejtyaqwetwy

On the way to building an integrated computational environment for the study of developmental patterns and genetic diseases

Andrei L Turinsky, Christoph W Sensen
2006 International Journal of Nanomedicine  
Our key approach to knowledge integration is a top-down mapping of data onto visual contexts.  ...  best matches a researcher's intuition.  ...  Acknowledgments This work has been supported by: Genome Canada through Genome Prairie's Integrated and Distributed Bioinformatics Platform Project; the Government of Canada and the Government of Alberta  ... 
doi:10.2147/nano.2006.1.1.89 pmid:17722266 pmcid:PMC2426770 fatcat:rjexut6cfjhbpj26zf4rpvjs7u

Constructing patch-based ligand-binding pocket database for predicting function of proteins

Lee Sael, Daisuke Kihara
2012 BMC Bioinformatics  
Given a query pocket in a protein, Patch-Surfer searches a database of known pockets and finds similar ones to the query.  ...  Methods: In our previous work, we have developed an alignment free local surface-based pocket comparison method, named Patch-Surfer, which predicts ligand molecules that are likely to bind to a protein  ...  Two options were tested for the matching stage: the first approach matches all patches while the other approach matches only patches that are more similar than the predefined distance threshold value.  ... 
doi:10.1186/1471-2105-13-s2-s7 pmid:22536870 pmcid:PMC3375630 fatcat:w2e4tgiitncatoyu5invflzukm

Registering Drosophila embryos at cellular resolution to build a quantitative 3D atlas of gene expression patterns and morphology

C.C. Fowlkes, C.L. Luengo Hendriks, S.V.E. Keranen, M.D. Biggin, D.W. Knowles, D. Sudar, J. Malik
2005 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)  
We report on a method for registering 3D expression data from different Drosophila embryos stained for overlapping subsets of gene products in order to build a composite atlas, ultimately containing coexpression  ...  The Berkeley Drosophila Transcription Network Project is developing a suite of methods to convert volumetric data generated by confocal fluorescence microscopy into numerical, three dimensional representations  ...  We overcome this problem by using a richer spatial descriptor termed shape context (see Figure 2 ) which has been successfully applied to a range of 2D and 3D shape matching problems in computer vision  ... 
doi:10.1109/csbw.2005.118 dblp:conf/csb/FowlkesMHKBKS05 fatcat:vv4gsqeh7nct7lfgeg2flh3guq

BioInfo3D: a suite of tools for structural bioinformatics

M. Shatsky, O. Dror, D. Schneidman-Duhovny, R. Nussinov, H. J. Wolfson
2004 Nucleic Acids Research  
The input to all services is either protein PDB codes or protein structures uploaded to the server. All the services areavailable at  ...  It does not require an a priori knowledge of the flexible hinge regions. MultiProt and MASS perform simultaneous comparison of multiple protein structures.  ...  ACKNOWLEDGEMENTS We thank our Structural Bioinformatics Group and the system team at Tel Aviv University.  ... 
doi:10.1093/nar/gkh413 pmid:15215437 pmcid:PMC441551 fatcat:t5fv5jzdkvgpxbewy6iiicmwxa

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

Maxim Totrov
2011 BMC Bioinformatics  
Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB.  ...  A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported.  ...  This article has been published as part of BMC Bioinformatics Volume 12 Supplement 1, 2011: Selected articles from the Ninth Asia Pacific Bioinformatics Conference (APBC 2011).  ... 
doi:10.1186/1471-2105-12-s1-s35 pmid:21342566 pmcid:PMC3044291 fatcat:ippsb4f5jnbdphy3osgw2usg44

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images

Sandhya P. Tiwari, Florence Tama, Osamu Miyashita
2018 BMC Bioinformatics  
Results: We developed the protocol to assemble a non-redundant set of 3D shapes for generating the 2D image library, and to retrieve potential match 3D shapes for query images, using EM data as a test.  ...  Conclusions: Through our computational method, we are able to quickly retrieve a 3D shape from a few 2D projection images.  ...  SASTBX is another tool that uses a database of 3D shapes to propose 3D models matching the SAXS data [35] .  ... 
doi:10.1186/s12859-018-2358-0 pmid:30208849 pmcid:PMC6134691 fatcat:vloanxjbzvdtfkm7tu5ott24ci

Bioinformatics---an introduction for computer scientists

Jacques Cohen
2004 ACM Computing Surveys  
The article aims to introduce computer scientists to the new field of bioinformatics.  ...  The underlying motivation for many of the bioinformatics approaches is the evolution of organisms and the complexity of working with incomplete and noisy data.  ...  ACKNOWLEDGMENTS The author wishes to express his gratitude to Mark Gerstein, Nathan Goodman and the reviewers who provided many suggestions to improve the original manuscript.  ... 
doi:10.1145/1031120.1031122 fatcat:i5au72xpujffrgryx3vnyiyeyy

MOTIF DISCOVERY WITH DATA MINING IN 3D PROTEIN STRUCTURE DATABASES: DISCOVERY, VALIDATION AND PREDICTION OF THE U-SHAPE ZINC BINDING ("HUF-ZINC") MOTIF

SEBASTIAN MAURER-STROH, HE GAO, HAO HAN, LIES BAETEN, JOOST SCHYMKOWITZ, FREDERIC ROUSSEAU, LOUXIN ZHANG, FRANK EISENHABER
2013 Journal of Bioinformatics and Computational Biology  
motifÀ À Àfunction relationships as the¯nding of the U-shape (Huf-Zinc) motif, originally a small student's project, exempli¯es.  ...  Proteins have evolved a series of motifs to speci¯cally recognize and bind zinc ions.  ...  Acknowledgment The authors acknowledge A*STAR for funding this research.  ... 
doi:10.1142/s0219720013400088 pmid:23427990 fatcat:lezpiqkdqbd6vbhomp7bcrh2ri

Bioinformatics in Proteomics: A Review on Methods and Algorithms

I. Popov, A. Nenov, P. Petrov, D. Vassilev
2009 Biotechnology & Biotechnological Equipment  
It is often said that bioinformatics is a knowledge based discipline.  ...  This means that many of the search and prediction methods that have been used to greatest effect in bioinformatics exploit information that has already been accumulated about the problem of interest, rather  ...  From this pair of matching residues an alignment is built with regular dynamic programming in order to give a score for the matching of every other pair of residues.  ... 
doi:10.1080/13102818.2009.10817624 fatcat:4dep7nrinrhiffrnhqxgf36bbq

3D Shape Description and Matching Based on Properties of Real Functions [article]

Silvia Biasotti, Bianca Falcidieno, Patrizio Frosini, Daniela Giorgi, Claudia Landi, Simone Marini, Giuseppe Patané, Michela Spagnuolo
2007 Eurographics State of the Art Reports  
This tutorial covers a variety of methods for 3D shape matching and retrieval that are characterized by the use of a real-valued function defined on the shape (mapping function) to derive its signature  ...  The methods are discussed following an abstract conceptual framework that distinguishes among the three main components of these class of shape matching methods: shape analysis, via the application of  ...  Acknowledgements This work has been partially supported by the EC-IST FP6 Network of Excellence AIM@SHAPE. Models are courtesy of the AIM@SHAPE repository http://www.aimatshape.net.  ... 
doi:10.2312/egt.20071071 fatcat:kunadx2snzhwzncsxyla675kfy
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