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Hierarchical protein structure superposition using both secondary structure and atomic representations

A P Singh, D L Brutlag
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
In this paper we present a new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level.  ...  We also performed searches of a representative set of the Protein Data Bank (PDB) using our program and detected structurally similarity between several distantly related proteins.  ...  The authors thank Russ Altman, Thomas Wu, Barry Robson, Brian Curless, Bernd Froehlich, and Tamara Shannon for their valuable discussions and editing assistance.  ... 
pmid:9322051 fatcat:t2lrfa3wizflhgpbutyrfmlhgq

Comparative Evaluation of Shape Retrieval Methods on Macromolecular Surfaces: An Application of Computer Vision Methods in Structural Bioinformatics

Mickael Machat, Florent Langenfeld, Daniela Craciun, Léa Sirugue, Taoufik Labib, Nathalie Lagarde, Maxime Maria, Matthieu Montes, Alfonso Valencia
2021 Bioinformatics  
the use of shape retrieval methods to screen large database of protein structures to identify surficial homologs and possible interacting partners, 3) opens an extension of the protein structure-function  ...  This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that 1) abstracts the underlying protein sequence, structure or fold, 2) allows  ...  , i.e. the fold and secondary structures encoded in the backbone atoms 3D coordinates.  ... 
doi:10.1093/bioinformatics/btab511 pmid:34247232 pmcid:PMC8652110 fatcat:zry564cz3rfwvnsmcuowi5cow4

Protein Structure Classification [chapter]

2012 Protein Bioinformatics  
I review the properties of protein structures, with a special interest on their geometry. Computer methods for the automatic comparison and classification of these structures are then reviewed.  ...  In parallel, I describe the existing classifications of protein structures, and their applications in biology, with a special focus on computational biology.  ...  Acknowledgments PK acknowledges support from the National Science Foundation (Grant CCR-00-86013) and from the National Institute of Health (GM 63817).  ... 
doi:10.1002/9780470092620.ch14 fatcat:m26yqasr3vcuxaxuwel2d75yey

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation

Ana Medina, Josep Triviño, Rafael J. Borges, Claudia Millán, Isabel Usón, Massimo D. Sammito
2020 Acta Crystallographica Section D: Structural Biology  
ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful.  ...  The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight.  ...  Secondary-and tertiary-structure annotation All algorithms in ALEPH rely on the geometrical representation of the main chain of a protein using a discrete distribution of CVs.  ... 
doi:10.1107/s2059798320001679 pmid:32133985 pmcid:PMC7057218 fatcat:sjlnhcbbhbe33jrww4baqnqnfy

RNA Bricks—a database of RNA 3D motifs and their interactions

Grzegorz Chojnowski, Tomasz Waleń, Janusz M. Bujnicki
2013 Nucleic Acids Research  
The algorithm compares spatial positions of backbone atoms of the user-provided query structure and of stored RNA motifs, without relying on sequence or secondary structure information.  ...  The RNA Bricks database (http://iimcb.genesilico. pl/rnabricks), stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA-protein  ...  We also thank Katarzyna Mikolajczak for help in the preparation of RNA contact annotation scripts, and Grzegorz Lach for suggesting the reduced graph representation of the RNA secondary structure to be  ... 
doi:10.1093/nar/gkt1084 pmid:24220091 pmcid:PMC3965019 fatcat:vswu4deignemlgoh7gxw7hz6v4

Multiple protein structure alignment

William R. Taylor, Tomas P. Flores, Christine A. Orengo
1994 Protein Science  
A method was developed to compare protein structures and to combine them into a multiple structure consensus.  ...  As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures, This leads to a hierarchic  ...  Cartoons of the secondary structural elements are presented as schematic representations produced by the program TOPS (Flores et al., 1994) . a-Helices are represented by circles and @-strands by triangles  ... 
doi:10.1002/pro.5560031025 pmid:7849601 pmcid:PMC2142613 fatcat:d5jfn7pxird2le7crzsuzy4d5m

Superimpose: a 3D structural superposition server

R. A. Bauer, P. E. Bourne, A. Formella, C. Frommel, C. Gille, A. Goede, A. Guerler, A. Hoppe, E.-W. Knapp, T. Poschel, B. Wittig, V. Ziegler (+1 others)
2008 Nucleic Acids Research  
Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins.  ...  The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at:  ...  Without the use of free and/or open source software  ... 
doi:10.1093/nar/gkn285 pmid:18492720 pmcid:PMC2447795 fatcat:c7ljn4uj6fbsxmmu4qfcwdirqi

Recent improvements in prediction of protein structure by global optimization of a potential energy function

J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D. R. Ripoll, R. Kazmierkiewicz, S. Oldziej, W. J. Wedemeyer, K. D. Gibson, Y. A. Arnautova, J. Saunders, Y.-J. Ye (+1 others)
2001 Proceedings of the National Academy of Sciences of the United States of America  
Recent improvements of a hierarchical ab initio or de novo approach for predicting bothandstructures of proteins are described.  ...  Whereas ␤ structures can now be predicted with the new procedure, the success rate for ␣͞␤and ␤-proteins is lower than that for ␣-proteins at present.  ...  Institutes of Health (GM-14312), the National Science Foundation (MCB95-13167), the Fogarty Foundation (R03 TW1064), the National Institutes of Health National Center for Research Resources (P41RR-04293), and  ... 
doi:10.1073/pnas.041609598 pmid:11226239 pmcid:PMC30138 fatcat:qek2bkxhpjgavj6sah763aqhcq

UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data

Rafal Adamczak, Jarek Meller
2016 BMC Bioinformatics  
Results: uQlust is a versatile and easy-to-use tool for ultrafast ranking and clustering of macromolecular structures. uQlust makes use of structural profiles of proteins and nucleic acids, while combining  ...  analysis, while yielding results on par with traditional approaches for both proteins and RNAs.  ...  Mahendra Thapa's help with generating structure sets used for benchmarking, and Mr. Prakash Velayutham's technical help.  ... 
doi:10.1186/s12859-016-1381-2 pmid:28031034 pmcid:PMC5198500 fatcat:vwhs3msgd5g2peyvqci5pyedxy

A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly

Gilad Wainreb, Nurit Haspel, Haim J. Wolfson, Ruth Nussinov
2006 Computer applications in the biosciences : CABIOS  
Motivation: Secondary-Structure Guided Superposition tool (SSGS) is a permissive secondary structure-based algorithm for matching of protein structures and in particular their fragments.  ...  To create a library, BBs generated by cutting proteins from the PDB are compared and structurally similar BBs are clustered.  ...  endorsement by the US Government.  ... 
doi:10.1093/bioinformatics/btl098 pmid:16543273 fatcat:lc4v2sdrpzbh5f3cbjgnymicnm

Distance-based indexing of residue contacts for protein structure retrieval and alignment

Ahmet Sacan, I. Hakki Toroslu, Hakan Ferhatosmanoglu
2008 2008 8th IEEE International Conference on BioInformatics and BioEngineering  
However, we are still far from having the right methods for sensitive and effective use of the available structural data.  ...  New protein structures are continuously being determined with the hope of deriving insights into the function and mechanisms of proteins, and consequently, protein structure repositories are growing by  ...  In order to capture both structural and biochemical information, each contact residue is further annotated with both its amino acid type and its secondary structure state.  ... 
doi:10.1109/bibe.2008.4696701 dblp:conf/bibe/SacanTF08 fatcat:bce2akwdgrgh7cd4rf4ikehzby

Algorithmic Methodologies for Discovery of Nonsequential Protein Structure Similarities [chapter]

Bhaskar DasGupta, Joseph Dundas, Jie Liang
2013 Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics  
An increasing number of protein structures are becoming available that either have no known function or whose functional mechanism is unknown or incomplete.  ...  Protein sequence comparisons have been used as a straightforward method for functional inheritance.  ...  ACKNOWLEDGMENTS DasGupta and Liang was partially supported by NSF grant DBI-1062328.  ... 
doi:10.1002/9781118567869.ch15 fatcat:tnbrdqdlerdfbezgm2vlnthtqy

Multipolar representation of protein structure

Apostol Gramada, Philip E Bourne
2006 BMC Bioinformatics  
Bridging the gap between atomic-level structure and overall protein-level functionality requires parameterizations of the protein structure (and other physicochemical properties) in a quasi-continuous  ...  We demonstrate that the multipoles can be used for the quantitative description of the protein shape and for the comparison of protein structures at various levels of detail.  ...  Acknowledgements We are grateful to Marian Anghel and Eric Scheeff for very useful discussions and to Yuting Jia for providing the programs for the spatial superposition of aligned structures.  ... 
doi:10.1186/1471-2105-7-242 pmid:16674828 pmcid:PMC1483839 fatcat:rroounveabbmdhhyi7nrkwt2ea

Protein Structure Classification [chapter]

Patrice Koehl
2006 Reviews in computational chemistry  
I review the properties of protein structures, with a special interest on their geometry. Computer methods for the automatic comparison and classification of these structures are then reviewed.  ...  In parallel, I describe the existing classifications of protein structures, and their applications in biology, with a special focus on computational biology.  ...  Acknowledgments PK acknowledges support from the National Science Foundation (Grant CCR-00-86013) and from the National Institute of Health (GM 63817).  ... 
doi:10.1002/0471780367.ch1 fatcat:ykk7nbob4fbc5awgqlscved4ua

Protein structure: geometry, topology and classification

William R Taylor, Alex C W May, Nigel P Brown, András Aszódi
2001 Reports on progress in physics (Print)  
Following an analysis of the current state of the classification of proteins, more abstract geometric and topological representations are explored, including the occurrence of knotted topologies.  ...  The structural principals of proteins are reviewed and analysed from a geometric perspective with a view to revealing the underlying regularities in their construction.  ...  Acknowledgments David Jones and Jaap Heringa are thanked for help with some of the figures.  ... 
doi:10.1088/0034-4885/64/4/203 fatcat:l6fpa5l4v5cz5mwhehc3m5iqyi
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