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Shape modeling and matching in identifying protein structure from low-resolution images

Sasakthi S. Abeysinghe, Tao Ju, Wah Chiu, Matthew Baker
2007 Proceedings of the 2007 ACM symposium on Solid and physical modeling - SPM '07  
Abstract In this paper, we describe a novel, shape-modeling approach to recovering 3D protein structures from volumetric images.  ...  Figure 1 : Identifying α-helices in a low-resolution protein image, using the Human Insulin Receptor -Tyrosine Kinase Domain (1IRK) as an example.  ...  Acknowledgements This research was supported in part by the National Science Foundation (EIA-0325004) and by the National Center for Research Resources (P41RR02250 and P20RR020647).  ... 
doi:10.1145/1236246.1236278 dblp:conf/sma/AbeysingheJCB07 fatcat:ss4rzcllhfcv7anlztkctxeiwq

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images

Sandhya P. Tiwari, Florence Tama, Osamu Miyashita
2018 BMC Bioinformatics  
In this study, we propose a quick strategy to retrieve potential 3D shapes, as low-resolution models, from a few 2D experimental images by searching a library of 2D projection images generated from existing  ...  We found that our ability to identify 3D shapes that match the query images depends on how complex the outline of the 2D shapes are and whether they are represented in the search image library.  ...  One application is the modeling from low-resolution cryo-EM maps, where computational modeling tools are used to generate detailed structural models that conform to low-resolution maps.  ... 
doi:10.1186/s12859-018-2358-0 pmid:30208849 pmcid:PMC6134691 fatcat:vloanxjbzvdtfkm7tu5ott24ci

BSP-SLIM: A blind low-resolution ligand-protein docking approach using predicted protein structures

Hui Sun Lee, Yang Zhang
2011 Proteins: Structure, Function, and Bioinformatics  
We developed BSP-SLIM, a new method for ligand-protein blind docking using low-resolution protein structures.  ...  docking conformations are then constructed by shape and chemical match of ligand with the negative image of binding pockets.  ...  Since most drug target proteins have no experimental structure available, a challenging issue is how one can generate reliable docking results using low-resolution models from protein structure predictions  ... 
doi:10.1002/prot.23165 pmid:21971880 pmcid:PMC3240723 fatcat:v3bawfu56fgfjc2yl3opuw4s3y

Interpretation of very low resolution X-ray electron-density maps using core objects

Philipp Heuser, Gerrit G. Langer, Victor S. Lamzin
2009 Acta Crystallographica Section D: Biological Crystallography  
A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density  ...  A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 Å is presented.  ...  This research was supported in part by the EC FP6-funded BIOXHIT project (contract No. LSHG-CT-2003-503420) and by the NIH R01 GM62612 grant through a postdoctoral fellowship to PH.  ... 
doi:10.1107/s090744490901991x pmid:19564689 pmcid:PMC2703575 fatcat:j7p6yhhrg5e7lo4tjmsfnhr47a

Novel Methods for Rapid Comparison and Multimeric Protein Complex Fitting for Low-Resolution Electron Microscopy Data

Lee Sael, Juan Esquivel-Rodriguez, Daisuke Kihara
2011 Biophysical Journal  
Here, we apply the 3DZD for comparing low-resolution structure data from the electron microscopy (EM). Two applications are presented.  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary Tabu  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary  ... 
doi:10.1016/j.bpj.2010.12.1962 fatcat:omiqxzzpwbdnrijmq7n3a3pcga

Scanning Transmission Electron Microscopy of Eukaryotic Cells in Liquid

Niels de Jonge, Madeline J. Dukes, Elizabeth A. Ring, Diana B. Peckys
2011 Biophysical Journal  
Here, we apply the 3DZD for comparing low-resolution structure data from the electron microscopy (EM). Two applications are presented.  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary Tabu  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary  ... 
doi:10.1016/j.bpj.2010.12.1964 fatcat:gnoprzphxbc5rcbre54wjf3lge

Orbweaver: A New Graphical User Interface for Particle Selection in Single-Particle Reconstruction with Cryo-Em

Robert Ezra Langlois, Joachim Frank
2011 Biophysical Journal  
Here, we apply the 3DZD for comparing low-resolution structure data from the electron microscopy (EM). Two applications are presented.  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary Tabu  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary  ... 
doi:10.1016/j.bpj.2010.12.1965 fatcat:7yijo3lzfnd2bar36rnk2qu4dy

Helex: an Evolutionary Tabu Search Strategy for the Identification of Helical Regions in cryo-Electron Microscopy Reconstructions

Mirabela Rusu, Stefan Birmanns
2011 Biophysical Journal  
Here, we apply the 3DZD for comparing low-resolution structure data from the electron microscopy (EM). Two applications are presented.  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary Tabu  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary  ... 
doi:10.1016/j.bpj.2010.12.1963 fatcat:zvh7wxja3nd4zcnj7oqiun4cqa

Computational methods for constructing protein structure models from 3D electron microscopy maps

Juan Esquivel-Rodríguez, Daisuke Kihara
2013 Journal of Structural Biology  
The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution  ...  Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures  ...  JER is a Fulbright Science and Technology Fellow.  ... 
doi:10.1016/j.jsb.2013.06.008 pmid:23796504 pmcid:PMC3795986 fatcat:mr3lorsn75akriotpmzs4be3ki

Shape modeling and matching in identifying 3D protein structures

Sasakthi Abeysinghe, Tao Ju, Matthew L. Baker, Wah Chiu
2008 Computer-Aided Design  
In this paper, we describe a novel geometric approach in the process of recovering 3D protein structures from scalar volumes.  ...  The input to our method is a sequence of α-helices that make up a protein, and a low-resolution protein density volume where possible locations of α-helices have been detected.  ...  Acknowledgements This research was supported in part by the National Science Foundation (EIA-0325004, IIS-0705538) and by the National Center for Research Resources (P41RR02250 and P20RR020647).  ... 
doi:10.1016/j.cad.2008.01.013 fatcat:w5myxztk4jgzxlddhqkpapofvm

The Molecular Architecture of Human Low Density Lipoprotein and Bound Receptor Revealed by Electron Cryo-Microscopy

Gang Ren, Gabby Rudenko, Steven J. Ludtke, Johann Deisenhofer, Henry J. Pownall, Wah Chiu
2010 Biophysical Journal  
Especially the docking of atomic models into low-to intermediate resolution volumetric data from cryo-electron microscopy has grown into an established technique over the last decade.  ...  LDL is heterogeneous in composition, shape, size, density and charge and is difficult for structural study by X-ray crystallization and NMR.  ...  Applying our approach to uncover mechanisms of allostery in human interleukin-2 and other proteins, we identify clusters of correlated residues from 50 ns of molecular dynamics simulations (see figure  ... 
doi:10.1016/j.bpj.2009.12.2070 fatcat:3tzsy6p6b5d6znemert7z2spwy

Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition

Hannah Ochner, Sven Szilagyi, Sabine Abb, Joseph Gault, Carol V. Robinson, Luigi Malavolti, Stephan Rauschenbach, Klaus Kern
2021 Proceedings of the National Academy of Sciences of the United States of America  
High-resolution imaging of protein structures following native ESI is thus of fundamental interest for establishing the relation between gas phase and solution structure.  ...  Taking advantage of low-energy electron holography's (LEEH) unique capability of imaging individual proteins with subnanometer resolution, we investigate the conformational flexibility of Herceptin, a  ...  Argyris Politis and Kjetil Hansen for providing us with their simulated models of collapsed antibodies and Dr. Jean-Nicolas Longchamp for his support in constructing our LEEH microscope.  ... 
doi:10.1073/pnas.2112651118 pmid:34911762 pmcid:PMC8713884 fatcat:csnqlsrfubgirnb65p4flihj5a

Fabs Enable Single Particle cryoEM Studies of Small Proteins

Shenping Wu, Agustin Avila-Sakar, JungMin Kim, David S. Booth, Charles H. Greenberg, Andrea Rossi, Maofu Liao, Xueming Li, Akram Alian, Sarah L. Griner, Narinobu Juge, Yadong Yu (+8 others)
2012 Structure  
One fundamental limitation is that images of small proteins embedded in vitreous ice do not contain adequate features for accurate image alignment.  ...  Structure Single Particle cryoEM of Small Proteins Structure 20, 582-592, April 4,  ...  Frankel), and 1P50 GM073210 (Membrane Protein Expression Center to R.M.S.), the UCSF Program for Breakthrough Biomedical Research (Opportunity Award in Basic Science and New Technology Award to Y.C.),  ... 
doi:10.1016/j.str.2012.02.017 pmid:22483106 pmcid:PMC3322386 fatcat:hel4ksfv7zcejnkjupfwqtw5ha

Using Sculptor for the Simultaneous Assembly of Atomic Components into Volumetric Maps

Stefan Birmanns
2011 Biophysical Journal  
Here, we apply the 3DZD for comparing low-resolution structure data from the electron microscopy (EM). Two applications are presented.  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary Tabu  ...  Overall, we show that the 3DZD is powerful in comparing low-resolution structure data for comparison and multiple-docking guided by the low-resolution data. 1751-Pos Board B661 Helex: an Evolutionary  ... 
doi:10.1016/j.bpj.2010.12.1966 fatcat:nwgk3l6ylfgf5aym6hlu4ou63a

Peptide-Conjugation Induced Conformational Changes in Human IgG1 Observed by Optimized Negative-Staining and Individual-Particle Electron Tomography

Huimin Tong, Lei Zhang, Allan Kaspar, Matthew J. Rames, Liqing Huang, Gary Woodnutt, Gang Ren
2013 Scientific Reports  
Shengli Zhang, and Mrs. James Song for their discussion and editing comments.  ...  DE-AC02-05CH11231) and partially supported by the William Myron Keck Foundation (no: 011808), QB3-Pfizer research grant (no: P0030609 and P0024086), and National Heart, Lung, and Blood Institute of the  ...  from the sample embedded in vitreous ice and imaged under low-dose conditions.  ... 
doi:10.1038/srep01089 pmid:23346347 pmcid:PMC3549606 fatcat:yqra4pdd55c6njasvt6l6maxwm
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