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PAST: fast structure-based searching in the PDB

H. Taubig, A. Buchner, J. Griebsch
2006 Nucleic Acids Research  
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

Wei-Cheng Lo, Ping-Chiang Lyu
2008 Genome Biology  
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

Andreas Martin Lisewski, Olivier Lichtarge
2006 Nucleic Acids Research  
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

W. W. Li
2001 Nucleic Acids Research  
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

W. W. Li
2002 Nucleic Acids Research  
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

Sebastian Bittrich, Stephen K. Burley, Alexander S. Rose, Marco Punta
2020 PLoS Computational Biology  
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

I. N. Shindyalov, P. E. Bourne
1998 Protein Engineering Design & Selection  
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]

Sebastian Bittrich, Stephen K. Burley, Alexander S. Rose
2020 bioRxiv   pre-print
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

Ilya N. Shindyalov, Philip E. Bourne
1997 Bioinformatics  
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

Yutaka Kuroda, Kazutoshi Tani, Yo Matsuo, Shigeyuki Yokoyama
2000 Protein Science  
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

Peter J. Artymiuk, Helen M. Grindley, Julie E. Park, David W. Rice, Peter Willett
1992 FEBS Letters  
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

Valentin M. Tabakmakher, Nikolay A. Krylov, Alexey I. Kuzmenkov, Roman G. Efremov, Alexander A. Vassilevski
2019 Scientific Data  
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

Jean-Francois St-Pierre, Normand Mousseau
2011 Biophysical Journal  
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

Alexei A Podtelezhnikov, David L Wild
2008 Source Code for Biology and Medicine  
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

Frantisek Pavelcik
2003 Acta Crystallographica Section A Foundations of Crystallography  
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
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