A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
Hierarchical protein structure superposition using both secondary structure and atomic representations
1997
Proceedings. International Conference on Intelligent Systems for Molecular Biology
Preserved Fulltext
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
2021
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2020
Acta Crystallographica Section D: Structural Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2013
Nucleic Acids Research
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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
1994
Protein Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2008
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2001
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2008; you can also visit the original URL.
The file type is application/pdf.
Recent improvements of a hierarchical ab initio or de novo approach for predicting both ␣ and  structures 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
2016
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2006
Computer applications in the biosciences : CABIOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2008
2008 8th IEEE International Conference on BioInformatics and BioEngineering
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2008; you can also visit the original URL.
The file type is application/pdf.
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]
2013
Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2006
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2006
Reviews in computational chemistry
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2006; you can also visit the original URL.
The file type is application/pdf.
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
2001
Reports on progress in physics (Print)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2006; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 1,167 results