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.
Filters
PAST: fast structure-based searching in the PDB
2006
Nucleic Acids Research
Preserved Fulltext
PAST is a new web service providing fast structural queries of the Protein Data Bank. ...
The search procedure is completely independent of the amino acid sequence of the polypeptide chains. ...
As well as the improved search functions by Uwe Römers and Anselm Kusser. We al thank the anonymous reviewers for helpful considerations. ...
doi:10.1093/nar/gkl273
pmid:16844992
pmcid:PMC1538836
fatcat:2la22nwrtnflxinsbvislhmuui
CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships
2008
Genome 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 2017; you can also visit the original URL.
The file type is application/pdf.
Circular permutation of a protein can be visualized as if the original amino-and carboxyl termini were linked and new ones created elsewhere. ...
We thank the authors of the BLAST and FAST algorithms, which were extensively used in this study. ...
Acknowledgements This work was supported by the National Science Council, Taiwan, ROC (NSC grant numbers: 95-3112-B-007-006 and 96-3112-B-007-006). ...
doi:10.1186/gb-2008-9-1-r11
pmid:18201387
pmcid:PMC2395249
fatcat:gubcjh2phjcnnlswrd6pxpkoxu
Rapid detection of similarity in protein structure and function through contact metric distances
2006
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 2011; you can also visit the original URL.
The file type is application/pdf.
The contact metric was the fastest method and its sensitivity, at any given specificity level, was a close second only to Fast Alignment and Search Tool-a structural alignment method that is slower by ...
The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. ...
Keck Center for Computational and Structural Biology (A.M.L). ...
doi:10.1093/nar/gkl788
pmid:17130161
pmcid:PMC1702494
fatcat:rvueilcgo5bctoqhvxtprtt3qq
CKAAPs DB: a conserved key amino acid positions database
2001
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 2004; you can also visit the original URL.
The file type is application/pdf.
Thus the database contains over 5000 representative polypeptide chains, covering all known structures in the PDB. ...
A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. ...
ACKNOWLEDGEMENTS This work was supported by the National Biomedical Computation Resource (NIH P41 RR 08605-06), National Science Foundation grant DBI 9808706 and Microstructure Image-Based Collaboratory ...
doi:10.1093/nar/29.1.329
pmid:11125128
pmcid:PMC29811
fatcat:hvxxkui36nae7fzmgytlwd7kce
CKAAPs DB: a Conserved Key Amino Acid Positions DataBase
2002
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 2004; you can also visit the original URL.
The file type is application/pdf.
Thus the database contains over 5000 representative polypeptide chains, covering all known structures in the PDB. ...
A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. ...
ACKNOWLEDGEMENTS This work was supported by the National Biomedical Computation Resource (NIH P41 RR 08605-06), National Science Foundation grant DBI 9808706 and Microstructure Image-Based Collaboratory ...
doi:10.1093/nar/30.1.409
pmid:11752351
pmcid:PMC99066
fatcat:y7x3a6rw3rew7g2k2l2yj2qzdi
Real-time structural motif searching in proteins using an inverted index strategy
2020
PLoS Computational 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.
Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids. ...
Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting ...
We also thank Florian Kaiser for sharing his expertise on structural motif searching and for providing the abstract depiction of amino acids and nucleotides, Michael Schroeder for noting the connection ...
doi:10.1371/journal.pcbi.1008502
pmid:33284792
fatcat:6lskbkc7vreqdcdw5j6swjnm74
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
1998
Protein Engineering Design & Selection
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.
The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. ...
Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http://cl.sdsc.edu/ce.html. ...
Acknowledgements This work was supported by grant DBI 9630339 from the National Science Foundation. ...
doi:10.1093/protein/11.9.739
pmid:9796821
fatcat:uf7wqm6ihjekponv3wztguliqm
Real-time structural motif searching in proteins using an inverted index strategy
[article]
2020
bioRxiv
pre-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 2020; you can also visit the original URL.
The file type is application/pdf.
Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids. ...
Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting ...
We are grateful to Florian Kaiser for sharing his expertise on structural motif searching and for providing the abstract depiction of amino acids and nucleotides. ...
doi:10.1101/2020.09.11.293977
fatcat:qzxwtcodinco5i4q4lfelt4tdm
Protein data representation and query using optimized data decomposition
1997
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 2002; you can also visit the original URL.
The file type is application/pdf.
In addition, collections of indices representing a particular property are maintained and can be queried for specific property patterns found across the whole database. ...
(III) A database supporting real-time 3-dimensional substructure searching will be reported elsewhere. Binaries of (I) and (III) are available for local use by contacting the authors. Contact: ...
Acknowledgments This work was supported by the National Science Foundation grant number BIR 9507625. We are grateful to Calton Pu for his careful review of this manuscript. ...
doi:10.1093/bioinformatics/13.5.487
fatcat:hfopul4e25ep5itrszzqmky4ee
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics
2000
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.
and have sizes suitable for fast structural analyses. ...
We thus have developed a program that reorganizes the output of BLAST searches and detects regions with a large number of similar sequences. ...
for discussion and advice, S. Miyazaki for visual inspection of SCOP linkers and discussion, and members of the Protein Research Group for discussion. PASS can be accessed at www. bio.gsc.riken.go.jp. ...
doi:10.1110/ps.9.12.2313
pmid:11206052
pmcid:PMC2144534
fatcat:wyo56weqibeuxkrtbnp5q6gree
Three-dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph-theoretical techniques
1992
FEBS Letters
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.
iJsing 3-D searching techniques based on algorithms derived from graph theory we have established a striking structural similarity between the structure of bovine carboxypeptidase A and that of the C-terminal ...
There is no signilicant sequence homology between the aminopeptidases and the carboxypeptidases but the strong structural relationship detected in this complex fold suggesls that there may be a very remote ...
The program (which is named PROTE) allows very fast searches of all the structures in the PDf3 for similarities, either partial or complete, to the search protein structure [9] . ...
doi:10.1016/0014-5793(92)80475-v
pmid:1592116
fatcat:5j4tzw5trngo5hqelmszqxlioa
Kalium 2.0, a comprehensive database of polypeptide ligands of potassium channels
2019
Scientific Data
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.
In addition to small molecules, there is a wide selection of several hundred polypeptide ligands binding to potassium channels, the majority of which have been isolated from animal venoms. ...
Potassium channels are the most diverse group of ion channels in humans. They take vital parts in numerous physiological processes and their malfunction gives rise to a range of pathologies. ...
Chugunov (Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia) for discussions concerning the database development. ...
doi:10.1038/s41597-019-0074-x
pmid:31133708
pmcid:PMC6536513
fatcat:y6us5hw6q5f7teymyevwkoowxq
Loop Conformation Prediction through Saddle-Point Search Simulations using the Art Nouveau Method and OPEP Simplified Potential
2011
Biophysical Journal
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.
An in silico approach followed with in vitro confirmation and in vivo evaluation is a starting point for developing new anti-malarial therapies. ...
In addition to identification of substrates, we are taking a fragmentbased approach to design new inhibitors. ...
In essence, they solve the problem of protein folding for a fragment of the structure to predict and have a computational cost proportional to the level of approximation of their energy potential. ...
doi:10.1016/j.bpj.2010.12.1396
fatcat:4p7wnqnukfcnnitc4izw4vlvge
CRANKITE: A fast polypeptide backbone conformation sampler
2008
Source Code for Biology and Medicine
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.
CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. ...
Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length. ...
Acknowledgements This work was supported by the National Institutes of Health Grant Number 1 P01 GM63208. ...
doi:10.1186/1751-0473-3-12
pmid:18577227
pmcid:PMC2443148
fatcat:a6bphnwmm5alph6avsa6ppw2re
Automatic model building based on flexible fragment formalism. The case of high-resolution protein structures
2003
Acta Crystallographica Section A Foundations of Crystallography
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.
A concept of¯exible fragments has been developed for automatic building of crystal structures. ...
Six monopeptides were designed as search fragments in a phased rotation and translation function for protein building. ...
The author is indebted to the University of Texas, Southwestern Medical Center at Dallas for ®nancial support. The research was supported by grants NIH GM 53163 (USA) and VEGA MS 1/7264/20 (SR). ...
doi:10.1107/s0108767303016830
pmid:12944613
fatcat:ejq6ol26kze2bjgdas64ghqu64
« Previous
Showing results 1 — 15 out of 3,643 results