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Clustering techniques for protein surfaces

L. Baldacci, M. Golfarelli, A. Lumini, S. Rizzi
2006 Pattern Recognition  
Surface-based techniques for protein comparison typically require applying clustering algorithms to the punctual 3D description of the surface in order to produce a compact surface representation, capable  ...  In this paper, we propose a formalization of the requirements for surface clustering in the biochemical context and present two different clustering techniques that meet them, based, respectively, on region-growing  ...  requirements for surface clustering in the biochemical domain, in preparing the mutation chains, and in validating the clustering and classification results.  ... 
doi:10.1016/j.patcog.2006.02.024 fatcat:cnhidete7ndphgxcf3ve3hrata

PROTEIN: A Visual Interface for Classification of Partial Reliefs of Protein Molecular Surfaces

Keiko NISHIYAMA, Takayuki ITOH
2008 The Journal of the Institute of Image Electronics Engineers of Japan  
We propose a visual interface to effectively visualize the partial reliefs of molecular surfaces of proteins. This technique assumes that molecule surfaces are approximated as triangular meshes.  ...  The presented technique then visualizes the clustering results applying a hierarchical data visualization technique "HeiankyoView", as a visual interface to explore the clustered partial reliefs.  ...  Kengo Kinoshita with the University of Tokyo, for overall valuable suggestion for the calculation of structural similarity of the protein molecular surfaces. We appreciate to Prof.  ... 
doi:10.11371/iieej.37.181 fatcat:qbcrfure3zgihggdcvazzwk57i

A Template-Matching Approach for Protein Surface Clustering

L. Baldacci, M. Golfarelli, A. Lumini, S. Rizzi
2006 18th International Conference on Pattern Recognition (ICPR'06)  
Surface-based techniques for protein comparison and classification typically require a compact surface representation, capable of effectively condensing its description.  ...  The effectiveness of our clustering algorithm in capturing surface similarities is then discussed within a larger framework for protein classification based on surface comparison, with the support of tests  ...  Discussion In this paper we proposed a clustering technique for protein surfaces aimed at creating homogeneous and regular surface patches for protein classification purposes.  ... 
doi:10.1109/icpr.2006.183 dblp:conf/icpr/BaldacciGLR06 fatcat:bvj5rgjahjbm5nuluadugcnbna

Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

Michael G. Lerner, Kristin L. Meagher, Heather A. Carlson
2008 Journal of Computer-Aided Molecular Design  
These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.  ...  In particular, a Jarvis-Patrick method is outlined for grouping the final locations of minimized probes into physical clusters.  ...  Spronk for their help in determining the appropriate JP parameters. We also thank Spronk for his assistance in writing and documenting the Python scripts.  ... 
doi:10.1007/s10822-008-9231-6 pmid:18679808 pmcid:PMC2856601 fatcat:rbguczbuvfblrfku5bhdwf3lse

Adhesive-free colloidal probes for nanoscale force measurements: Production and characterization

M. Indrieri, A. Podestà, G. Bongiorno, D. Marchesi, P. Milani
2011 Review of Scientific Instruments  
microscopy techniques.  ...  Research topics: -Development and implementation of atomic force microscopy techniques and methods; -Characterization of nanoscale physical and chemical properties of interfaces and systems by atomic force  ...  ; -Force-spectroscopy and force-imaging (force-distance and Force-Volume analyses) for the direct characterization of protein-surface interactions and of relevant surface properties (elasticity, adhesion  ... 
doi:10.1063/1.3553499 pmid:21361602 fatcat:uk4nniaqtnhfhggbgkztjtle7i

Understanding protein adsorption phenomena at solid surfaces

Michael Rabe, Dorinel Verdes, Stefan Seeger
2011 Advances in Colloid and Interface Science  
Protein adsorption at solid surfaces plays a key role in many natural processes and has therefore promoted a widespread interest in many research areas.  ...  Abstract Protein adsorption at solid surfaces plays a key role in many natural processes and has therefore promoted a widespread interest in many research areas.  ...  Acknowledgments The authors wish to thank the Swiss National Science Foundation (SNSF) for financial support.  ... 
doi:10.1016/j.cis.2010.12.007 pmid:21295764 fatcat:hxkt6clttzbhvnxuwb5kpdpc2a

Atomic force microscopy - looking at mechanosensors on the cell surface

J. J. Heinisch, P. N. Lipke, A. Beaussart, S. El Kirat Chatel, V. Dupres, D. Alsteens, Y. F. Dufrene
2012 Journal of Cell Science  
Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells.  ...  Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment.  ...  Table 1 . 1 Comparison of high-resolution techniques for imaging single proteins in cellsOnly whole cell analyses are considered, i.e. purified proteins or membranes are not included.  ... 
doi:10.1242/jcs.106005 pmid:23077172 pmcid:PMC3516434 fatcat:vinopampbvfw7jdxehcnwth2h4

Identification of Functional Surfaces of Proteins from Sequences

Jieling Zhao, Sema Kachalo, Zheng Ouyang, Jie Liang
2010 Biophysical Journal  
Such heterogeneity may have implications in regulating the ionic environment in bone responsible for bone remodeling. 3953-Plat SAXS: Structure Verification of an S-Layer Protein using a Fractal Mean Force  ...  Furthermore, we show that there is an intrinsic electromechanical heterogeneity in axial direction of individual fibrils that holds even for the collagen fibrils embedded in bone matrix.  ...  The identification of protein functional surfaces is important for understanding enzyme mechanism, protein function prediction, compound-protein docking, and drug design.  ... 
doi:10.1016/j.bpj.2009.12.4173 fatcat:zi7wvm6bmbfjrdpbgqglyd7qf4

Fuzzy clustering-based modeling of surface interactions and emulsions of selected whey protein concentrate combined to ι-carrageenan and gum arabic solutions

Murad Samhouri, Mahmoud Abu-Ghoush, Emad Yaseen, Thomas Herald
2009 Journal of Food Engineering  
In addition, a fuzzy-based clustering model was used to predict the surface properties.  ...  The fuzzy model achieved accuracies of (94%, 97%, 98%, and 94%) for predicting (EAI, ESI, surface tension, and interfacial tension), respectively.  ...  In addition, a subtractive clustering-based fuzzy models for predicting the surface properties of whey protein, was constructed.  ... 
doi:10.1016/j.jfoodeng.2008.07.029 fatcat:zvngwdsq4netzb3smfrkdc23de

SAXS: Structure Verification of an S-Layer Protein using a Fractal Mean Force Potential

Christine Horejs, Dietmar Pum, Uwe B. Sleytr, Rupert Tscheliessnig
2010 Biophysical Journal  
Such heterogeneity may have implications in regulating the ionic environment in bone responsible for bone remodeling. 3953-Plat SAXS: Structure Verification of an S-Layer Protein using a Fractal Mean Force  ...  Furthermore, we show that there is an intrinsic electromechanical heterogeneity in axial direction of individual fibrils that holds even for the collagen fibrils embedded in bone matrix.  ...  The identification of protein functional surfaces is important for understanding enzyme mechanism, protein function prediction, compound-protein docking, and drug design.  ... 
doi:10.1016/j.bpj.2009.12.4171 fatcat:rqsa7qejajafncjdbqqmhcasa4

Self-Organization of the Escherichia Coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy

Ann McEvoy, Derek Greenfield, Hari Shroff, Gavin E. Crooks, Ned S. Wingreen, Eric Betzig, Jan Liphardt
2010 Biophysical Journal  
Such heterogeneity may have implications in regulating the ionic environment in bone responsible for bone remodeling. 3953-Plat SAXS: Structure Verification of an S-Layer Protein using a Fractal Mean Force  ...  Furthermore, we show that there is an intrinsic electromechanical heterogeneity in axial direction of individual fibrils that holds even for the collagen fibrils embedded in bone matrix.  ...  The identification of protein functional surfaces is important for understanding enzyme mechanism, protein function prediction, compound-protein docking, and drug design.  ... 
doi:10.1016/j.bpj.2009.12.4175 fatcat:4oa44vul7rhybizynzopi4qeeq

Is Theory Leading Neutron Diffraction in Macromolecular Solvent Networks?

Timothy Fenn, Michael Schnieders, Vijay Pande, Axel Brunger
2010 Biophysical Journal  
Such heterogeneity may have implications in regulating the ionic environment in bone responsible for bone remodeling. 3953-Plat SAXS: Structure Verification of an S-Layer Protein using a Fractal Mean Force  ...  Furthermore, we show that there is an intrinsic electromechanical heterogeneity in axial direction of individual fibrils that holds even for the collagen fibrils embedded in bone matrix.  ...  The identification of protein functional surfaces is important for understanding enzyme mechanism, protein function prediction, compound-protein docking, and drug design.  ... 
doi:10.1016/j.bpj.2009.12.4172 fatcat:3jkohqlaizcwbg6b3v4cc4cakm

Ellipsoidal Abstract and Illustrative Representations of Molecular Surfaces

Meng Liang, Yuhang Fu, Ruibo Gao, Qiaoqiao Wang, Junlan Nie
2019 International Journal of Molecular Sciences  
In the paper, we improved the smoothness of transition for these abstractions by constructing a complete binary tree of a protein.  ...  The post-processing techniques applied, diffuse shading and contours, further conceal the expansion problem and highlight the surface details.  ...  ., materials used for experiments). Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms20205158 pmid:31627445 pmcid:PMC6834147 fatcat:2stwdfm5trhsncmwr4fdi6fgke

New directions in nanoscience: new challenges for surface analysis

R. E. Palmer
2002 Surface and Interface Analysis  
One example of a new surface analysis technique, scanning probe energy-loss spectroscopy, is discussed, along with specific ideas for further innovations.  ...  This paper considers the challenges for surface analysis presented by the creation of new types of nanometre-scale structure.  ...  For example, one can imagine the design and production of an artificial binding site-of controlled shape and functionality-for an individual protein molecule via the construction of a surface feature in  ... 
doi:10.1002/sia.1242 fatcat:ysaf7oa74vcjnknj7aahwof6mu

Indexing methods for efficient protein 3D surface search

Sungchul Kim, Sael Lee, Hwanjo Yu
2012 Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics - DTMBIO '12  
This paper exploits efficient indexing techniques for protein structure search where protein structures are represented as vectors by 3D-Zernike Descriptor (3DZD). 3DZD compactly represents a surface shape  ...  In addition, we introduce an extended approach for protein structure search based on indexing techniques that uses the 3DZD characteristic.  ...  Sael et al. introduced a new approach for fast protein surface similarity search using 3DZDs [18] .  ... 
doi:10.1145/2390068.2390078 dblp:conf/cikm/KimSY12 fatcat:yw64r5v7qvd4faxo4xavmak24y
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