Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

Esquivel‐Rodríguez, Juan; Kihara, Daisuke

doi:10.1021/jp212612t

Cited by 42 publications

(31 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Because of the speed, the method is particularly effective for fitting multiple subunits into an EM map. Along a similar line, our group has used the 3DZD for representing the shape of EM maps in the EMLZerD algorithm (Esquivel-Rodríguez and Kihara, 2012). EMLZerD fits multiple high-resolution structures into an EM map.…”

Section: Rigid Fitting Methodsmentioning

confidence: 99%

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

Esquivel‐Rodríguez

2013

Journal of Structural Biology

Self Cite

View full text Add to dashboard Cite

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3 Å. Computational methods play a key role in interpreting EM data. 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 from a 3D EM density map that is constructed from two-dimensional (2D) maps. 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 EM map. A list of available computational tools is also provided.

show abstract

Section: Rigid Fitting Methodsmentioning

confidence: 99%

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

Esquivel‐Rodríguez

2013

Journal of Structural Biology

Self Cite

View full text Add to dashboard Cite

show abstract

“…An overview of these translational grid-based FFT search schemes can be found in [9]. In recent approaches, the equispaced grid has been replaced with a non-equispaced Cartesian one, as in [3], or a polar one, as in [10, 13, 38, 44]. Fast translational matching exploits the fact that for each rotation, the objective function is a correlation integral, and can be computed by fast Fourier transforms.…”

Section: Related and Prior Workmentioning

confidence: 99%

Nonuniform Fourier Transforms for Rigid-Body and Multidimensional Rotational Correlations

Bajaj

Bauer

Bettadapura

et al. 2013

SIAM J. Sci. Comput.

View full text Add to dashboard Cite

The task of evaluating correlations is central to computational structural biology. The rigid-body correlation problem seeks the rigid-body transformation (R, t), R ∈ SO(3), t ∈ ℝ3 that maximizes the correlation between a pair of input scalar-valued functions representing molecular structures. Exhaustive solutions to the rigid-body correlation problem take advantage of the fast Fourier transform to achieve a speedup either with respect to the sought translation or rotation. We present PFcorr, a new exhaustive solution, based on the non-equispaced SO(3) Fourier transform, to the rigid-body correlation problem; unlike previous solutions, ours achieves a combination of translational and rotational speedups without requiring equispaced grids. PFcorr can be straightforwardly applied to a variety of problems in protein structure prediction and refinement that involve correlations under rigid-body motions of the protein. Additionally, we show how it applies, along with an appropriate flexibility model, to analogs of the above problems in which the flexibility of the protein is relevant.

show abstract

“…Two novel methods dealing with multimeric protein complexes were introduced by Daisuke Kihara (Purdue University): Multi-LZerD [40] for modeling the structure of protein complexes and EMLZ-erD [41] for fitting them into electron microscopy maps.…”

Section: Protein Structure and Functionmentioning

confidence: 99%

Summary of talks and papers at ISCB-Asia/SCCG 2012

et al. 2013

View full text Add to dashboard Cite

The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG).45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement.In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.

show abstract

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

Cited by 42 publications

References 47 publications

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

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

Nonuniform Fourier Transforms for Rigid-Body and Multidimensional Rotational Correlations

Summary of talks and papers at ISCB-Asia/SCCG 2012

Contact Info

Product

Resources

About