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This paper introduces GLUBs, which are games based on molecular mechanisms that take place in biological systems. Such games make use of interactive 3D graphics, and allow the player to interact with molecular components using simple 2D mouse gestures. They are similar to puzzle games, since the goal is to discover the correct interactions between molecular components. When the correct interactions are found, the player observes a molecular mechanism taking place. GLUBs thus have the potentialdoi:10.1145/1920778.1920795 dblp:conf/fplay/Pintilie10 fatcat:dd4oouvg4jbyvcajq2le463rm4
more »... o communicate much of the growing structural and biochemical knowledge in a fun and interesting way. In the game presented in this paper, the molecular mechanism involves the assisted folding of a protein by a chaperone.
Lecture Notes in Computer Science
We present a graphical user interface that allows an artist to virtually design and visualize net sculptures. Net sculptures consist of net pieces that are seamlessly connected to each other and to fixed rails. They are flexible and hence dynamic under external forces such as gravity and wind. The interface that we describe allows an artist to create net sculptures made up of multiple net pieces. Simple operations such as clicking on points and click-and-drag gestures are used to create anddoi:10.1007/978-3-642-13544-6_7 fatcat:miklx46eujeu5c3vizospoehxy
more »... fy individual net pieces, and drag-and-drop gestures are used to connect net pieces to multiple rails. The effect of gravity on the net sculpture is simulated, allowing the artist to simultaneously design and visualize net sculptures as they would appear once installed in a real setting.
CryoEM density maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryoEM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands, and other solvent atoms, using models fitted to or derived from cryoEM maps. Q-scores can also be averaged to representdoi:10.1101/722991 fatcat:btop4ms5uvagthfi3gjzpfx6by
more »... features such as entire residues and nucleotides. In several examples, Q-scores are shown to correlate well to resolvability. Q-scores averaged over entire models are also shown to correlate closely to the estimated resolution of cryoEM maps for both protein and RNA. Assuming the models they are calculated from are well-fitted to the map, Q-scores can thus be used as another measure to indicate the quality or resolvability in entire maps and also of features as small as individual atoms.
Michael Rossmann was a pioneer in combining X-ray crystallography and cryoEM maps. In his early papers in this area, he described how to score a model fitted to a map by looking at the density value at each atom; the density value for the atom was obtained by averaging the values at the nearest grid points in the map. Another measure he described was to consider whether the density value at the atom's position was negative, and hence not resolved [1, 2] . Prof. Rossmann wrote and maintaineddoi:10.1017/s1431927621005146 fatcat:gk5wrwobnzdm5eytckijx3rpha
more »... to calculate such scores, while searching for good fits of a model in a map, part of a method called EMFit. He was happy to share and explain how to run the code to interested researchers, including ourselves; we had many conversations and 'remote' sessions (which were then less common), where he showed us how to run the code and how it worked. The methods became very useful to us as we also explored the combination of X-ray structures and cryoEM maps.
D77 Pintilie and Chiu Validation of cryo-EM structures 11 of 11 ... D77 of 11 Pintilie and Chiu Validation of cryo-EM structures Acta Cryst. (2021). D77 of 11 Pintilie and Chiu Validation of cryo-EM structures Acta Cryst. (2021). ...doi:10.1107/s2059798321006069 pmid:34473085 pmcid:PMC8411978 fatcat:ikwmefph2rdexo62iuqmqi2ppm
AbstractBreakthroughs in single-particle cryo-electron microscopy (cryo-EM) technology have made near-atomic resolution structure determination possible. Here, we report a ∼1.35-Å structure of apoferritin reconstructed from images recorded on a Gatan K3 or a Thermo Fisher Falcon 4 detector in a commonly available 300-kV Titan Krios microscope (G3i) equipped with or without a Gatan post-column energy filter. Our results demonstrate that the atomic-resolution structure determination can bedoi:10.1101/2020.08.19.256909 fatcat:n7k5qpnwyrcqzfjkgqahyfylaa
more »... d by single-particle cryo-EM with a fraction of a day of automated data collection. These structures resolve unambiguously each heavy atom (C, N, O, and S) in the amino acid side chains with an indication of hydrogen atoms' presence and position, as well as the unambiguous existence of multiple rotameric configurations for some residues. We also develop a statistical and chemical based protocol to assess the positions of the water molecules directly from the cryo-EM map. In addition, we have introduced a B' factor equivalent to the conventional B factor traditionally used by crystallography to annotate the atomic resolution model for determined structures. Our findings will be of immense interest among protein and medicinal scientists engaging in both basic and translational research.
Then phenix.real_space_refine and Coot (Emsley et al. 2010) were 274 applied for model optimization. 275 The final model was evaluated by MolProbity (Chen et al. 2010) and Q-scores (Pintilie et al.) ... mobile as indicated in the resolution map(Figure 1-135figure supplement 2E) and Q score(Figure 2-supplement 2), which measures the local136 resolution (Kucukelbir et al. 2014) and structure resolvability (Pintilie ...doi:10.1101/2020.04.29.068361 fatcat:ksuvngvsn5fr5jszxfsyw5gzai
As a national facility, it is imperative that we are able to get the most out of each user's data collection session. This includes optimization of high-resolution single particle data collection throughput and quality, by optimizing data collection parameters for each user's samples. This starts with selection of the microscope used for data collection. The Stanford-SLAC cryoEM Center (S 2 C 2 ) has three Thermo Scientific Titan Krios G3i electron microscopes equipped with either a K3 withdoi:10.1017/s1431927621004359 fatcat:xhuxf6c73bhkzi4t5zuf7owipi
more »... gy filter (Gatan, Inc), or a Falcon 4 (Thermo Scientific) direct electron detector. While users mostly have a preference for one system over the other, we have demonstrated the ability to achieve structures at a resolution of 1.34Å and 1.36Å, from our Krios equipped with either an energy-filtered Gatan K3, or Thermo Scientific Falcon 4 detector without an energy filter, respectively  . For these structures we used ~8,000 movies (~900,000 particles) collected over 16 hours for the K3 and ~7,700 movies (~500,000 particles) collected over 15 hours for the Falcon 4 ( Figure 1A ). We have also collected data with EER mode on the Falcon 4 which can extend the structure resolution to 1.27Å. Figure 2 shows a 3D density map with apparent side chain features.
Pintilie 3 , Eduardo Sanz Garcia 2 , Ingvar Lagerstedt 2 , Matthew L. Baker 3 , Raul Sala 1 , Steven J. Ludtke 3 , Helen M. ... role at the dimerization interface and in the regulation of LRRK2 kinase activity. 1800-Pos 1801-Pos Board B693 Emdatabank: Unified Data Resource for 3DEM Catherine Lawson 1 , Ardan Patwardhan 2 , Grigore ...doi:10.1016/j.bpj.2012.11.1950 fatcat:qk4dnhm3nncrzmd7ux6lpmo3um
The discovery and design of biologically important RNA molecules is dramatically outpacing three-dimensional structural characterization. To address this challenge, we present Ribosolve, a hybrid method integrating moderate-resolution cryo-EM maps, chemical mapping, and Rosetta computational modeling, and demonstrate its application to thirteen previously unknown 119- to 338-nucleotide protein-free RNA-only structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate,doi:10.1101/717801 fatcat:risdasbvd5glngda3rjbnpzvle
more »... l-length V. cholerae and F. nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and computer-designed spinach-TTR-3, eterna3D-JR_1, and ATP-TTR-3 with and without AMP. Blind challenges, prospective compensatory mutagenesis, internal controls, and simulation benchmarks validate the Ribosolve models and establish that modeling convergence is quantitatively predictive of model accuracy. These results demonstrate that RNA-only 3D structure determination can be rapid and routine.
Chains 497 representing α-and β-tubulin subunits were respectively fitted to groups of 2 regions (with the 498 V-shape) with the SegFit tool in Segger (Pintilie et al., 2010). ... The fits with the top score 499 matched the map well, with secondary structures in the map and model agreeing well; Z-scores 500 were ~20 (Pintilie and Chiu, 2012), indicating high confidence the fit is ...doi:10.1101/2021.05.23.445366 fatcat:nmblrtoseva7vj2rxdqrpvnw6q
CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions,doi:10.1016/j.bpj.2015.11.3522 pmid:26743049 pmcid:PMC4775875 fatcat:bqxpik7f3jahvig2tj6hudvbgy
more »... h can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å ), whereas other components are at slightly lower resolutions: portal (9.2 Å ), hub (8.5 Å ), tailspike (10.9 Å ), and needle (10.5 Å ). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density.
Pintilie and Chiu Page 11 Figure 2. Pintilie and Chiu Page 12 J Struct Biol. Author manuscript; available in PMC 2019 December 01. Pintilie and Chiu Page 16 J Struct Biol. ... Pintilie and Chiu Page 18 J Struct Biol. Author manuscript; available in PMC 2019 December 01. Pintilie and Chiu Page 19 J Struct Biol. ...doi:10.1016/j.jsb.2018.08.015 pmid:30144506 pmcid:PMC6525962 fatcat:lqlffh5xhjcotderwqmlpbnp5y
Segmentation and docking are useful methods for discovery of molecular components in cryo-EM (Electron Cryo-Microscopy) density maps of macromolecular complexes. In this paper, we describe the segmentation and docking methods implemented in Segger. For 12 targets included in the 2010 Cryo-EM Modeling Challenge, we segmented the regions corresponding to individual molecular components using Segger. We then used the segmented regions to guide rigid-body docking of individual components. Andoi:10.1002/bip.22074 pmid:22696409 pmcid:PMC3402182 fatcat:u3hskusp4zh43cpv73qyvhnkcu
more »... ent in the accuracy of the component segmentation of the targets based on Segger and other methods was made by comparing the docking results of individual components to the segmented regions. The docking results were evaluated by comparison to published structures and by calculation of several scores including atom inclusion, density occupancy, and geometry clash. Keywords cryo-EM; segmentation; map based modeling Introduction Electron cryo-microscopy (cryo-EM) produces volumetric density maps that reveal the structure of a wide variety of macromolecular complexes at different resolutions. 1,2 Typically, a macromolecular complex is made up of multiple molecular components of the same or different proteins or nucleic acids. At high resolutions (~4.5 Å or better), C-alpha backbone of protein components can be built based on the map alone. 3 At lower resolutions, it is more typical to dock known molecular structures into the appropriate regions of the components within the complex to discover their conformations and their interactions among each other. At all resolutions, it is also useful to first segment the map into regions corresponding to individual molecular components before docking or de novo modeling. Various methods have been used for the segmentation of cryo-EM density maps, including watershed, 4 level sets, 5 and elastic networks. 6 We introduced a method based on watershed and scale space filtering, 7 which we have applied to the targets included in the 2010 cryo-EM challenge. This method has been developed as a plugin for the UCSF Chimera molecular visualization software. 8 We refer to this plugin module as Segger. In this paper, we compare segmentations produced with Segger and other segmentation results submitted to the challenge which were obtained using VolRover 5 and hENM. 6 We docked models of
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