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MSDmotif: exploring protein sites and motifs

Adel Golovin, Kim Henrick
2008 BMC Bioinformatics  
Results: We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database.  ...  It provides multiple views of data found in the PDB archive for exploring protein structures.  ...  Acknowledgements MSDmotif service is part of the BioSapiens project. funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health  ... 
doi:10.1186/1471-2105-9-312 pmid:18637174 pmcid:PMC2491636 fatcat:7rg254btwbfn5bim6534z6hr4y

seeMotif: exploring and visualizing sequence motifs in 3D structures

D. T.-H. Chang, T.-Y. Chien, C.-Y. Chen
2009 Nucleic Acids Research  
motifs to protein chains in structures.  ...  Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation.  ...  The second group focuses more on functional sites of biopolymers, such as catalytic sites and protein-DNA or protein-protein interaction sites.  ... 
doi:10.1093/nar/gkp439 pmid:19477961 pmcid:PMC2703912 fatcat:7wvyu7vxozfypnx2wf2p6bfexe

A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding

Will A Stanley, Niko V Pursiainen, Elspeth F Garman, André H Juffer, Matthias Wilmanns, Petri Kursula
2007 BMC Structural Biology  
Previously, structural data have been obtained from the TPR domain of Pex5p in both the liganded and unliganded states, indicating a conformational change taking place upon cargo protein binding.  ...  Results: We have used a range of biophysical and computational methods to further analyse the conformational flexibility and ligand binding of Pex5p.  ...  Gunter Schneider and Ylva Lindqvist for kindly supporting his work.  ... 
doi:10.1186/1472-6807-7-24 pmid:17428317 pmcid:PMC1854907 fatcat:7mfypyzogvdplmduuuxifhooea

ProSeg: a database of local structures of protein segments

Yoshito Sawada, Shinya Honda
2008 Journal of Computer-Aided Molecular Design  
As one of strategies, it is effective to consider a short segment, whose size is in between an amino acid and a domain, as a correlation unit for exploring the structure-to-sequence relationship.  ...  Integration of knowledge on the sequencestructure correlation of proteins provides a basis for the structural design of artificial novel proteins.  ...  ., MSS) and Mr. Hiroaki Ishikawa (MSS) for collaboration in developing the database system, and to Mr.  ... 
doi:10.1007/s10822-008-9248-x pmid:18931918 fatcat:espa72cs5fd2nhua5zj7l2lh3q

Structure Motivator: A tool for exploring small three-dimensional elements in proteins

David P Leader, E Milner-White
2012 BMC Structural Biology  
The software application, Structure Motivator, allows interactive exploration and analysis of such elements, and their resolution into sub-classes.  ...  The application has been applied both to classical motifs, such as the β-turn, and 'non-motif' structural elements, such as specific segments of helices.  ...  Acknowledgements We thank Attila Tajlil for migrating the MySQL database to Derby and the University of Glasgow for providing facilities for the work.  ... 
doi:10.1186/1472-6807-12-26 pmid:23067391 pmcid:PMC3507813 fatcat:k6rbbb4spzgjxad3jmne457uka

Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

Annalisa Marsico, Andreas Henschel, Christof Winter, Anne Tuukkanen, Boris Vassilev, Kerstin Scheubert, Michael Schroeder
2010 BMC Bioinformatics  
Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins.  ...  Conclusions: Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites.  ...  We thank Gihan Dawelbait for helping in functional annotation, Rainer Winnenburg and Dimitra Alexopoulou for critical reading of the manuscript. We thank the EU project Sealife for funding.  ... 
doi:10.1186/1471-2105-11-204 pmid:20420672 pmcid:PMC2876129 fatcat:r7xhbks42naqpbv76boa55w2pq

A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules

R. Huhne, F.-T. Koch, J. Suhnel
2007 Briefings in Functional Genomics & Proteomics  
3D structures of proteins, nucleic acids, carbohydrates and complexes thereof.  ...  As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for  ...  The authors are grateful to Kristina Mehliss who has helped with thumbnail image generation, to Friedrich Haubensak for maintaining the web server and to Stefan Westermeier for working on the QuickSearch  ... 
doi:10.1093/bfgp/elm020 pmid:17956938 fatcat:6mtu2bifpbarhorqxhkgq7xwna

PDBe: Protein Data Bank in Europe

S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman (+13 others)
2009 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe) (http://www .ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive  ...  The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe  ...  ACKNOWLEDGEMENTS We wish to thank all collaborators and partners in the EBI, EMBL, wwPDB and other collaborative efforts, as  ... 
doi:10.1093/nar/gkp916 pmid:19858099 pmcid:PMC2808887 fatcat:amgz3equ6jgenhym77vbghy47e

Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery

Sarika Kondra, Titli Sarkar, Vijay Raghavan, Wu Xu
2021 Frontiers in Chemistry  
The new motifs or substructures we identified specifically for proteases and kinases provide a deeper insight into their structural relations.  ...  Every substructure of one protein is compared to every other substructure in a different protein.  ...  ACKNOWLEDGMENTS We thank the support from Louisiana Board of Regents [LEQSF(2015-18)-RD-B-06] to WX and VR, and C. Dean Domingue and Noah P.  ... 
doi:10.3389/fchem.2020.602291 pmid:33520934 pmcid:PMC7838567 fatcat:cfk5krdxhrgw3o3from4rxpef4

Binding MOAD (Mother Of All Databases)

Liegi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner, Heather A. Carlson
2005 Proteins: Structure, Function, and Bioinformatics  
MSDMotif MSDmotif is a database which aims to provide a mechanism for querying the PDB about motifs.  ...  [66] This database contains all PDB ligands, their interactions with macromolecules (protein, DNA, and RNA), coordination, protein sequences, and ProSite motifs.  ...  The client tier is comprised of a standard web browser (such as Internet Explorer) which accesses the website over the Internet.  ... 
doi:10.1002/prot.20512 pmid:15971202 fatcat:qya7yxhipzes7ng3dgnc6da4au

Characterization of the Substrate Specificity and Mechanism of Protein Arginine Methyltransferase 1

Whitney Lyn Wooderchak
2009
Most PRMT1 substrates are methylated within repeating 'RGG' and glycine-arginine rich motifs.  ...  However, PRMT1 also methylates a single arginine on histone-H4 that is not embedded in a glycine-arginine motif, indicating that PRMT1 protein substrates are not limited to proteins with 'RGG' sequences  ...  Using the MSDmotif server at EMBL-EBI (http://www.ebi.ac.uk/msd-srv/msdmotif/), the pdb was queried for structures harboring potential PRMT1 methylation sites.  ... 
doi:10.26076/48ea-9d28 fatcat:vhfw7xtv6fdblitt3tnisvgpem