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Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction [chapter]

Brian Y. Chen, Viacheslav Y. Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas M. Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
2006 Lecture Notes in Computer Science  
We present a new approach, Geometric Sieving (GS), which refines candidate motifs into optimized motifs with maximal geometric and chemical dissimilarity from all known protein structures.  ...  One approach to predicting protein function is to search functionally uncharacterized protein structures (targets), for substructures with geometric and chemical similarity (matches), to known active sites  ...  Contributions and Outline We begin by describing the design and implementation of Geometric Sieving (GS), an algorithm for refining candidate motifs into optimized motifs.  ... 
doi:10.1007/11732990_42 fatcat:ywk3ly2cjrcadpt7oghhodc7ie

CAVITY SCALING: AUTOMATED REFINEMENT OF CAVITY-AWARE MOTIFS IN PROTEIN FUNCTION PREDICTION

BRIAN Y. CHEN, DREW H. BRYANT, VIACHESLAV Y. FOFANOV, DAVID M. KRISTENSEN, AMANDA E. CRUESS, MAREK KIMMEL, OLIVIER LICHTARGE, LYDIA E. KAVRAKI
2007 Journal of Bioinformatics and Computational Biology  
Algorithms for geometric and chemical comparison of protein substructure can be useful for many applications in protein function prediction.  ...  For the purpose of function prediction, the accuracy of motif matching algorithms can be evaluated with the number of statistically significant matches to functionally related proteins, true positives  ...  Introduction Geometric and chemical comparison of protein substructures can be applied to the problem of protein function prediction by identifying new sites that share geometric and chemical characteristics  ... 
doi:10.1142/s021972000700276x pmid:17589966 fatcat:dnlxq4crezhhvkpmtoigmbpbaa

The LabelHash algorithm for substructure matching

Mark Moll, Drew H Bryant, Lydia E Kavraki
2010 BMC Bioinformatics  
In the first phase the proteins are preprocessed in a fashion that allows for instant lookup of partial matches to any motif.  ...  There is an increasing number of proteins with known structure but unknown function.  ...  Fofanov for many useful discussions on the use of statistical analysis and for his comments on LabelHash. They are also deeply grateful for the help of B. Chen with MASH. This work has bene-  ... 
doi:10.1186/1471-2105-11-555 pmid:21070651 pmcid:PMC2996407 fatcat:tfzefchyevaqtiqt6hjnsxjclm

3D DNA Crystals and Nanotechnology

Paul Paukstelis, Nadrian Seeman
2016 Crystals  
A scaffold for crystallizing proteins could provide a unique method for overcoming the macromolecular crystallization bottleneck and enable rapid structure determination, thereby enhancing and accelerating  ...  A scaffold for crystallizing proteins could provide a unique method for overcoming the macromolecular crystallization bottleneck and enable rapid structure determination, thereby enhancing and accelerating  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cryst6080097 fatcat:k32fbfdphvdrnj7g45luxmntyy

Control of protein functional dynamics by peptide linkers

Willy Wriggers, Sugoto Chakravarty, Patricia A. Jennings
2005 Biopolymers  
Control of structural flexibility is essential for the proper functioning of a large number of proteins and multiprotein complexes.  ...  Absence of such motion, as in so-called molecular rulers, also has desirable functional effects in protein architecture.  ...  We thank Tetsuro Fujisawa for kindly providing the SAXS data of chimeric GFP proteins.  ... 
doi:10.1002/bip.20291 pmid:15880774 fatcat:t7zrwmdwuffoto3h4bwm57du24

New frontiers for the materials genome initiative

Juan J. de Pablo, Nicholas E. Jackson, Michael A. Webb, Long-Qing Chen, Joel E. Moore, Dane Morgan, Ryan Jacobs, Tresa Pollock, Darrell G. Schlom, Eric S. Toberer, James Analytis, Ismaila Dabo (+12 others)
2019 npj Computational Materials  
The Materials Genome Initiative (MGI) advanced a new paradigm for materials discovery and design, namely that the pace of new materials deployment could be accelerated through complementary efforts in  ...  in this new environment, examine how to effectively utilize new materials innovation infrastructure, and discuss challenges in achieving accelerated materials research through the seamless integration of  ...  The authors of this article feature the organizing committee and section coordinators. We thank Gabriela Basel for help in composing figures in this Article.  ... 
doi:10.1038/s41524-019-0173-4 fatcat:n7bbruv4gvb7ng3as4dmrz6k4e

Graphical Abstract: Angew. Chem. Int. Ed. 50/2020

2020 Angewandte Chemie International Edition  
Chemie Contents Am ild, deoxygenative fluorination approach was developed using only oxalyl chloride and potassium fluoride to access ab road variety of fluorinated phosphorus(V) compounds in neutral,  ...  Preparation of functionalized isotactic polypropylenes is hampered by the absence of good tacticity-inducing ligand motifs for group 10 catalysts.  ...  The dynamic DNA/protein complexes, composed of antibody-labelled DNA motifs (TB and B*C) and redox-labelled DNA (CR*), eliminate the need for multistep processing and allow sample-in-answer-out analysis  ... 
doi:10.1002/anie.202085011 fatcat:42w7qylxlfcx5h4ogamditz5xy

Graphisches Inhaltsverzeichnis: Angew. Chem. 50/2020

2020 Angewandte Chemie  
Preparation of functionalized isotactic polypropylenes is hampered by the absence of good tacticity-inducing ligand motifs for group 10 catalysts.  ...  The dynamic DNA/protein complexes, composed of antibody-labelled DNA motifs (TB and B*C) and redox-labelled DNA (CR*), eliminate the need for multistep processing and allow sample-in-answer-out analysis  ... 
doi:10.1002/ange.202085011 fatcat:vg5m5le7xzbmfgl4obulstocja

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
Wigley for the contribution to this work with the x-ray structure of the protein ligand to the GR1222222.  ...  Acknowledgements This research was partly funded by the EU FP7 project OpenTox -An Open Source Predictive Toxicology Framework (Health-F5-2008-200787) and the German Federal Ministry for the Environment  ...  direct geometric comparison of the protein structures.  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

Innovative Hybrid Materials with Improved Tensile Strength Obtained by 3D Printing [chapter]

Roxana Mioara Piticescu, Laura Madalina Cursaru, Gabriela Negroiu, Cristina Florentina Ciobota, Ciprian Neagoe, Daniel Safranchik
2020 Biomaterials [Working Title]  
motifs that independently contribute to the protein viscoelasticity.  ...  This property may be exploited to enhance the tensile strength of a 3D structure by adding specific synthetic polypeptides to the composition of the printing paste.  ...  Raluca Elena Irimescu (IMNR) for the experimental work performed during STSM stage at Technion-Israel Institute of Technology in the frame of COST Action CA 15102, CRM-EXTREME.  ... 
doi:10.5772/intechopen.91296 fatcat:zy2xorzvxrfrhabh4m544yxtva

High Throughput Methods in the Synthesis, Characterization, and Optimization of Porous Materials

Ivan G Clayson, Daniel Hewitt, Martin Hutereau, Tom Pope, Ben Slater
2020 Advanced Materials  
Porous materials are widely employed in a large range of applications, in particular, for storage, separation, and catalysis of fine chemicals.  ...  Whilst high throughput approaches have been used for more than 30 years in the porous material fields, routine integration of experimental and computational processes is only now becoming more established  ...  B.S. would also like to thank the Royal Society for an Industry Fellowship IF160062 and a studentship INF\PHD\180018 which also contributed to this review.  ... 
doi:10.1002/adma.202002780 pmid:32954550 fatcat:43qjqaflprfrtlz6y3z5lmkh74

Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches

Siegfried M. Musser, David Grünwald
2016 Journal of Molecular Biology  
the inherent properties of the FG-polypeptide distribution.  ...  upon activation of the RanGTPase by RanGAP and Ran binding proteins (RanBPs). [33] [34] [35] The FG-Network The FG-network has two main functions: it creates a permeability barrier that prevents the free  ...  Acknowledgments We thank Thomas Schwartz, Guo Fu, and Darryl Conte for discussions and proofreading, and Amir Tahmasbi, Jerry Chao, and Raimund Ober for assistance with Figure 9 and the section on biases  ... 
doi:10.1016/j.jmb.2016.02.023 pmid:26944195 pmcid:PMC4909493 fatcat:6q4y63nfnbgvhazchg5lfefqxu

An Overview of Biological Macromolecule Crystallization

Irene Russo Krauss, Antonello Merlino, Alessandro Vergara, Filomena Sica
2013 International Journal of Molecular Sciences  
bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions.  ...  This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which  ...  Acknowledgments The authors thank Lelio Mazzarella for his very helpful comments, suggestions, and valuable assistance in the preparation of this paper.  ... 
doi:10.3390/ijms140611643 pmid:23727935 pmcid:PMC3709751 fatcat:2xtnbda2tncsfekng4b4ctxihu

Modeling Kinetics of Subcellular Disposition of Chemicals

Stefan Balaz
2009 Chemical Reviews  
For the longer distribution periods, the depot function of proteins for chemicals with log P > 0 starts to play a role.  ...  Predictions for more-diverse chemicals required a 3D approach.  ... 
doi:10.1021/cr030440j pmid:19265398 pmcid:PMC2682929 fatcat:7ho2qyeddfdunpsxmqeetvgqfy

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

T. S. Baker, N. H. Olson, S. D. Fuller
1999 Microbiology and Molecular Biology Reviews  
The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions.  ...  The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens  ...  Unwin for teaching the intricacies of low-dose microscopy of unstained and vitrified specimens; D. Eisenberg, F. Eiserling, and D. L. D.  ... 
doi:10.1128/mmbr.63.4.862-922.1999 fatcat:lcs72ikrmvgevez5f2vuhujtze
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