Filters








888 Hits in 6.0 sec

Flexible image registration for the identification of best fitted protein models in 3D-EM maps

Laura Fernandez-de-Manuel, Maria J. Ledesma-Carbayo, Julian Atienza-Herrero, Carlos O. S. Sorzano, Jose-Maria Carazo, Andres Santos
2008 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
In this work we propose an image registration algorithm to automatically fit protein atomic domain models into medium-resolution three-dimensional electron microscopy reconstructions (3D-EM map).  ...  The approach employs a flexible registration algorithm whose optimizer controls the generation of stereo-chemically correct models from a given reference domain belonging to a super-family of proteins.  ...  In this article, we propose a registration algorithm that takes into account both flexible and rigid movements of the domain to fit in the 3D-EM map.  ... 
doi:10.1109/isbi.2008.4541163 dblp:conf/isbi/Fernandez-de-ManuelLASCS08 fatcat:cauwa4qczvd7bfefpldgxwixde

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  ...  This work was partly supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM075004, R01GM097528) and the National Science Foundation (IIS0915801, EF0850009  ... 
doi:10.1016/j.jsb.2013.06.008 pmid:23796504 pmcid:PMC3795986 fatcat:mr3lorsn75akriotpmzs4be3ki

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, Klaus Schulten
2008 Structure  
The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while  ...  The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are  ...  ACKNOWLEDGMENTS The authors would like to thank David Wells, Aleksei Aksimientiev, and Jim Phillips for help with the implementation of the MDFF method in NAMD; Jordi Cohen for stimulating discussions;  ... 
doi:10.1016/j.str.2008.03.005 pmid:18462672 pmcid:PMC2430731 fatcat:c6owcmt3nbblpkwrvyi4v7u24y

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics [chapter]

Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, Klaus Schulten
2018 Series in Structural Biology  
The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while  ...  The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are  ...  ACKNOWLEDGMENTS The authors would like to thank David Wells, Aleksei Aksimientiev, and Jim Phillips for help with the implementation of the MDFF method in NAMD; Jordi Cohen for stimulating discussions;  ... 
doi:10.1142/9789813234864_0044 fatcat:rkcgwsjbwngg7ejuifh2mub74u

Symmetry-Restrained Flexible Fitting for Symmetric EM Maps

Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, Klaus Schulten
2011 Structure  
In order to incorporate knowledge of structural symmetry into the fitting procedure, we developed the symmetry-restrained MDFF method.  ...  A number of methods for fitting atomic-scale structures into cryo-EM maps have been developed, including the molecular dynamics flexible fitting (MDFF) method.  ...  Acknowledgments This work was supported by grants from the National Institutes of Health (P41-RR005969) and the National Science Foundation (PHY0822613).  ... 
doi:10.1016/j.str.2011.07.017 pmid:21893283 pmcid:PMC3412758 fatcat:i47srl4otvd5hhhq7ke3mkb5w4

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N. Kinch, R. Dustin Schaeffer, Claudia Millán, Hahnbeom Park (+20 others)
2021 Science  
The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging X-ray crystallography and cryo-EM structure modeling  ...  We explored network architectures incorporating related ideas and obtained the best performance with a three-track network in which information at the 1D sequence level, the 2D distance map level, and  ...  The simultaneous processing of sequence, distance, and coordinate information by the threetrack architecture opens the door to new approaches incorporating constraints and experimental information at all  ... 
doi:10.1126/science.abj8754 pmid:34282049 pmcid:PMC7612213 fatcat:fk44kzhvengu7i73lkdp4veye4

Structure of the SLC4 transporter Bor1p in an inward-facing conformation

Nicolas Coudray, Sean L. Seyler, Ralph Lasala, Zhening Zhang, Kathy M. Clark, Mark E. Dumont, Alexis Rohou, Oliver Beckstein, David L. Stokes
2016 Protein Science  
This homology model was fitted to the cryo-EM density map using the Molecular Dynamics (MD) Flexible Fitting method and then relaxed by all-atom MD simulation in explicit solvent and membrane.  ...  Comparisons of the resulting Bor1p model with the Xray structure of AE1 in an outward-facing conformation, together with MD simulations of inwardfacing and outward-facing Bor1p models, suggest rigid body  ...  Computer simulations were run in part on TACC Stampede of the Extreme Science and Engineering Discovery Environment (XSEDE).  ... 
doi:10.1002/pro.3061 pmid:27717063 pmcid:PMC5192975 fatcat:2o7sutktnrcwtll3vppdcklxey

Brush Border Myosin–I Structure and ADP-dependent Conformational Changes Revealed by Cryoelectron Microscopy and Image Analysis

James D. Jontes, Ronald A. Milligan
1997 Journal of Cell Biology  
Comparison of the behavior of BBM-I with skeletal and smooth muscle subfragments-1 suggests that there are substantial differences in the structure and energetics of the biochemical transitions in the  ...  This has enabled us to model a high resolution structure of BBM-I using the crystal structures of the chicken skeletal muscle myosin catalytic domain and essential light chain.  ...  Milligan is an Established Investigator of the American Heart Association. J.D. Jontes is a predoctoral fellow of the Howard Hughes Medical Institute.  ... 
doi:10.1083/jcb.139.3.683 pmid:9348285 pmcid:PMC2141714 fatcat:rucjtfwgpbg6jjneyus2allfkq

FOLD-EM: automated fold recognition in medium- and low-resolution (4–15 Å) electron density maps

Mitul Saha, Marc C. Morais
2012 Computer applications in the biosciences : CABIOS  
If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map.  ...  As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.  ...  of FOLD-EM to do fitting incorporating the issue of partial matching seen in Fitting that incorporates conformation changes arising from domain movements Another unique aspect of FOLD-EM is its ability  ... 
doi:10.1093/bioinformatics/bts616 pmid:23131460 pmcid:PMC3519459 fatcat:k3g2pf7abvg4hn5wkm62422duy

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

J. I. Garzon, J. Kovacs, R. Abagyan, P. Chacon
2006 Bioinformatics  
Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map.  ...  Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger  ...  ACKNOWLEDGEMENTS The authors would like to thank J. M. Valpuesta [CNB(CSIC), Spain] for Prefoldin and F. Asturias (The Scripps Research Institute, USA)  ... 
doi:10.1093/bioinformatics/btl625 pmid:17150992 fatcat:cvy423bggzc4dofuw43kbtjvxi

Accurate prediction of protein structures and interactions using a 3-track network [article]

Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R. Dustin Schaeffer, Claudia Millán, Hahnbeom Park (+20 others)
2021 bioRxiv   pre-print
The 3-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems  ...  We explored network architectures incorporating related ideas and obtained the best performance with a 3-track network in which information at the 1D sequence level, the 2D distance map level, and the  ...  TS, CB and TPK acknowledge the ESRF (ID30-3, Grenoble, France) and DESY (P11, PETRAIII, Hamburg, Germany) for provision of synchrotron-radiation facilities and support during data collection.  ... 
doi:10.1101/2021.06.14.448402 fatcat:mx7dqz7uxzfxzgyvc6sfr7pcwm

Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily

Jiwei Liu, Matteo Tassinari, Diorge P. Souza, Souvik Naskar, Jeffrey K. Noel, Olga Bohuszewicz, Martin Buck, Tom A. Williams, Buzz Baum, Harry H. Low
2021 Cell  
Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers.  ...  This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries.  ...  ACKNOWLEDGMENTS We thank Diamond for access and support of the cryo-EM facilities at the UK National Electron Bio-Imaging Centre (eBIC) funded by the Wellcome Trust, MRC, and BBSRC.  ... 
doi:10.1016/j.cell.2021.05.041 pmid:34166615 pmcid:PMC8281802 fatcat:dvygnlc6cnbfpf7ognolp2pz7y

Exploring the spatial and temporal organization of a cell's proteome

Martin Beck, Maya Topf, Zachary Frazier, Harianto Tjong, Min Xu, Shihua Zhang, Frank Alber
2011 Journal of Structural Biology  
Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells.  ...  macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of  ...  Excellent PhD Thesis Award -Scientific Research Foundation of the Chinese Academy of Sciences (to S.Z.).  ... 
doi:10.1016/j.jsb.2010.11.011 pmid:21094684 pmcid:PMC3784337 fatcat:qx76diqpjnh2dlklxhp4tsq2by

Structural Architecture of the CARMA1/Bcl10/MALT1 Signalosome: Nucleation-Induced Filamentous Assembly

Qi Qiao, Chenghua Yang, Chao Zheng, Lorena Fontán, Liron David, Xiong Yu, Clay Bracken, Monica Rosen, Ari Melnick, Edward H. Egelman, Hao Wu
2013 Molecular Cell  
Combining crystallography, nuclear magnetic resonance, and electron microscopy, we reveal the structure of the Bcl10 CARD filament and the mode of interaction between CARMA1 and Bcl10.  ...  Structure-guided mutagenesis confirmed the observed interfaces in Bcl10 filament assembly and MALT1 activation in vitro and NF-κB activation in cells.  ...  support from the National Institutes of Health (R01AI089882 to H.W. and R01EB001567 to E.H.E.), Cancer Research Institute (Q.Q., C.Y., and L.D.), Spanish Ministry of Science and Innovation (L.F.), and  ... 
doi:10.1016/j.molcel.2013.08.032 pmid:24074955 pmcid:PMC3929958 fatcat:n5nf3ml5rjcr3ioa3c5dxdybyq

The structural basis for Z α1-antitrypsin polymerization in the liver

Sarah V. Faull, Emma L. K. Elliston, Bibek Gooptu, Alistair M. Jagger, Ibrahim Aldobiyan, Adam Redzej, Magd Badaoui, Nina Heyer-Chauhan, S. Tamir Rashid, Gary M. Reynolds, David H. Adams, Elena Miranda (+3 others)
2020 Science Advances  
and results from the formation and deposition of mutant forms of α1-antitrypsin as "polymer" chains in liver tissue.  ...  Moreover, there is little information on the relevance of well-studied artificially induced polymers to these disease-associated molecules.  ...  The Dim60, Dim90, and Dim60H maps have been deposited in the EMDB with accessions EMD-4632, EMD-4631, and EMD-4620. The crystal structure of Fab4B12 has been deposited as PDB accession 6QU9.  ... 
doi:10.1126/sciadv.abc1370 pmid:33087346 pmcid:PMC7577719 fatcat:ub6hlylfnnfqvlki3nir73ijae
« Previous Showing results 1 — 15 out of 888 results