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The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry

Wan Kyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder
2006 PLoS Computational Biology  
Citation: Kim WK, Henschel A, Winter C, Schroeder M (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol 2(9): e124.  ...  A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes.  ...  Funding through the EFRE (Europä ischer Fonds fü r regionale Entwicklung) projects CODI (Classification of Domain Interfaces), FoldUnfold, GoEverywhere, and the European Union IST projects Sealife and  ... 
doi:10.1371/journal.pcbi.0020124 pmid:17009862 pmcid:PMC1584320 fatcat:npvjydlqa5bcjpfvfmybphjxpq

The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry

Wan Kyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder
2005 PLoS Computational Biology  
Citation: Kim WK, Henschel A, Winter C, Schroeder M (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol 2(9): e124.  ...  A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes.  ...  Funding through the EFRE (Europä ischer Fonds fü r regionale Entwicklung) projects CODI (Classification of Domain Interfaces), FoldUnfold, GoEverywhere, and the European Union IST projects Sealife and  ... 
doi:10.1371/journal.pcbi.0020124.eor fatcat:cowc33cez5hgvjaxxijkvcatqu

A protein domain interaction interface database: InterPare

Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak
2005 BMC Bioinformatics  
for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition  ...  We introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net.  ...  We also thank all the scientists in the field of protein-protein interaction.  ... 
doi:10.1186/1471-2105-6-207 pmid:16122378 pmcid:PMC1236910 fatcat:xg2belho5vdv7cq4fmn2326tua

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

George R Bickerton, Alicia P Higueruelo, Tom L Blundell
2011 BMC Bioinformatics  
The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces.  ...  Results: Here we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions.  ...  GRJB thanks the BBSRC for funding this work. AH thanks UCB Celltech and BBRSC for funding the study of protein-protein interactions as drug targets.  ... 
doi:10.1186/1471-2105-12-313 pmid:21801404 pmcid:PMC3161047 fatcat:kw3gzdxlandejanhlyifkh3o4i

Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways

N. Rekha, S.M. Machado, C. Narayanan, A. Krupa, N. Srinivasan
2004 Proteins: Structure, Function, and Bioinformatics  
Using a data set of aligned protein domain superfamilies of known three-dimensional structure, we compared the location of interdomain interfaces on the tertiary folds between members of distantly related  ...  Based on the analysis of multidomain proteins of known or unknown structure, we suggest that variation in protein-protein interactions in members within a superfamily could serve as diverging points in  ...  ACKNOWLEDGMENTS Our thanks to Anirban Bhaduri for kindly providing us with the superfamily alignments and superpositions in the PASS2 database, to Shashi Pandit for providing flat files of the SUPFAM database  ... 
doi:10.1002/prot.20319 pmid:15562516 fatcat:mjmrku4fubf4babdungf2cksdu

Probing the Interactions of Porphyrins with Macromolecules Using NMR Spectroscopy Techniques

Ilche Gjuroski, Julien Furrer, Martina Vermathen
2021 Molecules  
This review focuses on such non-covalent interactions of porphyrinic drugs with synthetic polymers as well as with biomolecules such as phospholipids or proteins.  ...  Based on the advantage of providing structural and dynamic information with atomic resolution simultaneously, NMR spectroscopy is a powerful method for studying molecular interactions between porphyrinic  ...  The many different aspects of porphyrins such as synthesis, coordination chemistry, biochemistry, and applications have been compiled in a detailed compendium of numerous volumes devoted to this class  ... 
doi:10.3390/molecules26071942 pmid:33808335 fatcat:4x2uwobkejgunemhxbmcosjrcm

Acetylcholinesterase: From 3D structure to function

Hay Dvir, Israel Silman, Michal Harel, Terrone L. Rosenberry, Joel L. Sussman
2010 Chemico-Biological Interactions  
The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine.  ...  It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues.  ...  Acknowledgements This study was supported by the Nalvyco Foundation, the Bruce Rosen Foundation, the Jean and Jula Goldwurm Memorial Foundation, the Divadol Foundation, the Neuman Foundation, the Benoziyo  ... 
doi:10.1016/j.cbi.2010.01.042 pmid:20138030 pmcid:PMC2894301 fatcat:ba5n6rvrwjbvloyhec5t3vmsbi

Analysis of -1,3-Glucan Assembly in Saccharomyces cerevisiae Using a Synthetic Interaction Network and Altered Sensitivity to Caspofungin

G. Lesage
2004 Genetics  
A network core of 51 genes is multiply connected with 112 interactions.  ...  Integration of the glucan interaction network with the caspofungin data indicates an overlapping set of genes involved in FKS2 regulation, compensatory chitin synthesis, protein mannosylation, and the  ...  Gas1p, a GPI-anchored protein localized proteins with 16 predicted transmembrane domains that to the extracellular face of the plasma membrane, has share 88% identity.  ... 
doi:10.1534/genetics.167.1.35 pmid:15166135 pmcid:PMC1470839 fatcat:hp6v5gowife5npw2vndsc2bdgi

The forces at work in colloidal self-assembly: a review on fundamental interactions between colloidal particles

Qin Li, Ulrich Jonas, X. S. Zhao, Michael Kappl
2008 Asia-Pacific Journal of Chemical Engineering  
In this article, we provide an overview on the forces at work in a colloidal system, in particular, the roles of these forces at various stages in colloidal self-assembly.  ...  Van der Waals, electrostatic, hydrodynamic, and capillary forces, as well as Brownian motions, are extensively discussed, whereas other types of interactions are briefly introduced and summarized.  2008  ...  essentially many-body interactions.  ... 
doi:10.1002/apj.144 fatcat:wtybvolhhvdankzadxb5lrvnse

Bridging protein local structures and protein functions

Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2008 Amino Acids  
One of the major goals of molecular and evolutionary biology is to understand the functions of proteins by extracting functional information from protein sequences, structures and interactions.  ...  In this review, we summarize the repertoire of methods currently being applied and report recent progress in the field of in silico annotation of protein function based on the accumulation of vast amounts  ...  LYW and XSZ are also supported by the Grant No. 5039052006CB from the Ministry of Science and Technology, China. The research was also supported by NSFC-JSPS collaborative project No. 10711140116.  ... 
doi:10.1007/s00726-008-0088-8 pmid:18421562 fatcat:micrifjcrfetnafnm4fx45ouom

Morphological Pathways of Mitochondrial Division

Bernard Tandler, Charles Hoppel, Jason Mears
2018 Antioxidants  
Ongoing studies will continue to sort through the complex network of interactions that drive this critical event.  ...  Additionally, we highlight the major protein constituents that drive mitochondrial fission and the role of connections with the endoplasmic reticulum in establishing sites of membrane division.  ...  Conflicts of Interest: The authors have no conflicts of interest to declare.  ... 
doi:10.3390/antiox7020030 pmid:29462856 pmcid:PMC5836020 fatcat:y3hry24ylnf2vcjdhcgsxt5mmu

Life-science applications of the Cambridge Structural Database

Robin Taylor
2002 Acta Crystallographica Section D: Biological Crystallography  
CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein–ligand interaction is and what its geometry is likely to be.  ...  Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling ofin vivosituations, although the influence  ...  All staff of the Cambridge Crystallographic Data Centre, past and present, are thanked for their efforts in building and maintaining the CSD System.  ... 
doi:10.1107/s090744490200358x pmid:12037325 fatcat:uas2dhs54rcoteuagk5juzb53y

Viral Capsid Proteins Are Segregated in Structural Fold Space

Shanshan Cheng, Charles L. Brooks, Dennis R. Livesay
2013 PLoS Computational Biology  
medoids with a non-redundant subset of protein domains in the SCOP database, not including the viral capsid entries.  ...  Given the prevalence of the signature jelly-roll topology in viral capsid proteins, we are interested in whether these functionally unique capsid proteins are also structurally unique in terms of folds  ...  Conceived and designed the experiments: SC CLB. Performed the experiments: SC. Analyzed the data: SC CLB. Contributed reagents/ materials/analysis tools: SC CLB. Wrote the paper: SC CLB.  ... 
doi:10.1371/journal.pcbi.1002905 pmid:23408879 pmcid:PMC3567143 fatcat:zgx27d6yrzgqzlm7kxsm2fohfu

Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

Matthew J. O'Meara, Andrew Leaver-Fay, Michael D. Tyka, Amelie Stein, Kevin Houlihan, Frank DiMaio, Philip Bradley, Tanja Kortemme, David Baker, Jack Snoeyink, Brian Kuhlman
2015 Journal of Chemical Theory and Computation  
The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence recovery in protein design simulations, and  ...  The functional form of the H-bond potential is physically motivated and parameters are fit so that H-bond geometries that Rosetta generates closely resemble H-bond geometries in high-resolution crystal  ...  Computing was carried out using resources donated by the Google Exacycle for Visiting Faculty program (googleresearch.blogspot.com/2012/12/millions-of-core-hours-awarded-to.html).  ... 
doi:10.1021/ct500864r pmid:25866491 pmcid:PMC4390092 fatcat:drrs667gzjaqlpu6v72q6vermm

Properties of Titin Immunoglobulin and Fibronectin-3 Domains

Larissa Tskhovrebova, John Trinick
2004 Journal of Biological Chemistry  
The Z-line and M-line domains can bind to structural proteins of the respective sarcomere regions, as well as to cytoplasmic signaling molecules. A-band modules bind to major thick filament proteins.  ...  The unique sequences of the I-band part may also bind signaling molecules. The letter P indicates location of the phosphorylation sites.  ...  These residues are likely to control surface properties of the domains and thus to define their interactions at interfaces and binding to other proteins.  ... 
doi:10.1074/jbc.r400023200 pmid:15322090 fatcat:h3trthlz5vdfznrcqaxudcmgve
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