13 research outputs found
Side-Chain Entropy (SCE), <i>S<sub>sc</sub></i>, of 675 Nonhomologous Proteins in the PDB
<div><p>(A) Side-chain entropy versus chain length. Two results with <i>α</i> = 0.6 (red crosses) and 0.8 (green circles) are shown.</p><p>(B) Percentage of SCE contributed by buried residues versus chain length.</p></div
Performance of the Sequential Monte Carlo Method
<div><p>(A) Comparison of the SMC estimation with exhaustive enumeration for fragments of proteins 2ovo and 3ebx.</p><p>(B) Standard deviation of the SMC estimation for four different sample sizes, 100, 500, 1,000, and 2,000, respectively, calculated from 20 independent SMC runs. The first number in each parentheses pair is the number of residues of the protein, and the second number the average SCE of 20 runs with 1,000 samples in each run.</p></div
SCE of NMR and X-Ray Structures versus Rg
<div><p>Average SCE difference between X-ray and NMR structures (Δ<i>S<sub>XN</sub></i>) versus the average difference of radius of gyration between X-ray and NMR backbones (Δ<i>R<sub>g</sub></i>) for the 23 proteins.</p><p>×, proteins whose X-ray structures have much higher SCE than but similar <i>R<sub>g</sub></i> to the corresponding NMR structures.</p><p>Δ, proteins whose X-ray structures gain considerable SCE by packing a little looser.</p><p>○, proteins whose X-ray structures pack tighter than NMR structures but with comparable SCE.</p><p>+, small proteins of which both Δ<i>R<sub>g</sub></i> and Δ<i>S<sub>XN</sub></i> are small.</p></div
SCE of NMR and X-Ray Structures
<div><p>(A) Box plot for distributions of the absolute pairwise SCE difference (|Δ<i>S<sub>N</sub></i>|) of NMR structures of 23 proteins. Different coloured boxes indicate different ranges of average RMSDs of the structure pairs.</p><p>(B) Box plot for distributions of the SCE difference between X-ray and NMR structures (Δ<i>S<sub>XN</sub></i>) for 23 proteins. Different colours indicate different ranges of average RMSDs of the X-ray and NMR structure pairs. For proteins 1btv, 1vre, and 1ah2, <i>α</i> = 0.7 was used for both X-ray and NMR structures.</p></div
SCE of Native and Decoy Structures
<div><p>(A) SCE (<i>S<sub>sc</sub></i>) versus the radius of gyration (<i>R<sub>g</sub></i>).</p><p>(B) SCE (<i>S<sub>sc</sub></i>) versus the number of residue contacts (<i>N<sub>c</sub></i>), for protein <b>1ctf</b> and its decoys from the 4state_reduced decoy set.</p><p>(C) SCE (<i>S<sub>sc</sub></i>) versus the number of interfacial contacts for protein–protein complex <b>1spb</b> and its decoys.</p><p>(D) SCE (<i>S<sub>sc</sub></i>) versus the number of interfacial contacts for protein–protein complex <b>1brc</b> and its decoys.</p><p>The black dot is the native structure, blue triangles (<2.0 Å RMSD to the native structure) and green circles (>2.0 Å) are decoy structures. The SCE of protein complexes are calculated using <i>α</i> = 0.7 (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020168#s4" target="_blank">Methods</a>).</p></div
Statistical power of phylo-HMM for evolutionarily conserved element detection-5
<p><b>Copyright information:</b></p><p>Taken from "Statistical power of phylo-HMM for evolutionarily conserved element detection"</p><p>http://www.biomedcentral.com/1471-2105/8/374</p><p>BMC Bioinformatics 2007;8():374-374.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2194792.</p><p></p>ample "0.0510" means = 0.05 and = 10. The points are their power at posterior probability threshold equal to 0.5. The point corresponding to the baseline (P0.25L50) is indicated as a green dot. The blue solid lines connect the points with the same , while the red dashed line connects the points with the same . Some of the points are highlighted by crosses. The green dotted line crosses show the 1-to-3quartile range. The black solid line crosses show the 95% bootstrap confidence interval of the median sensitivity and specificity
Statistical power of phylo-HMM for evolutionarily conserved element detection-7
<p><b>Copyright information:</b></p><p>Taken from "Statistical power of phylo-HMM for evolutionarily conserved element detection"</p><p>http://www.biomedcentral.com/1471-2105/8/374</p><p>BMC Bioinformatics 2007;8():374-374.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2194792.</p><p></p>etic tree. The different lines represent the different branches as illustrated in the legend. (B) Relationships for branches in the symmetric star-topology tree. The different lines correspond to the different numbers of genomes (n) represented by the tree
Average intensities of the control channel data from 12 as a function of position-specific GC counts
Each 50-mer probe is partitioned into 5 equal parts of 10 nucleotides, and average intensities are computed as a function of GC counts in each part. Different colors represent different samples. The GC-related variations of intensities behave similarly across the five locations on probes, and we thus see that the GC effect is not position specific.<p><b>Copyright information:</b></p><p>Taken from "Model-based analysis of two-color arrays (MA2C)"</p><p>http://genomebiology.com/2007/8/8/R178</p><p>Genome Biology 2007;8(8):R178-R178.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2375008.</p><p></p
Gel Electrophoretic Mobility-Shift Analysis of SpoIIID Binding
<div><p>DNA fragments of interest were amplified by PCR, gel-purified, and end-labeled using [γ-<sup>32</sup>P]-ATP and polynucleotide kinase. Purified SpoIIID was added at increasing concentrations (0 nM for lanes 1 and 5, 50 nM for lane 2, 100 nM for lane 3, and 200 nM for lane 4) and incubated at room temperature for 30 min before loading on to a nondenaturing gel containing 6% polyacrylamide. With the exception of (D), the DNA fragments corresponded to the upstream regions of the indicated genes. See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020328#s4" target="_blank">Materials and Methods</a> for the identity (coordinates) of the specific DNA sequences used in the analyses.</p>
<p>(A) Gel shifts for known targets of SpoIIID (<i>bofA</i> and <i>spoIVCA</i>), representing positive controls, and genes (<i>abrB, spoIIGA,</i> and <i>racA</i>) under the control of another DNA-binding protein (Spo0A), representing negative controls.</p>
<p>(B) Gel shifts for genes identified as possible targets of SpoIIID by transcriptional profiling.</p>
<p>(C) Gel shift for <i>cotE</i>. Expression of <i>cotE</i> from its P2 promoter is strongly dependent on SpoIIID. No binding of SpoIIID to the upstream sequence for <i>cotE</i> is observed, suggesting that the effect of SpoIIID on transcription from the P2 promoter is indirect.</p>
<p>(D) Gel shifts for chromosomal regions strongly enriched for SpoIIID binding as judged by ChIP-on-chip analysis. For each region, four consecutive DNA fragments of approximately 400 nucleotides in length were analyzed.</p></div
The Mother-Cell Line of Gene Transcription
<div><p>(A) Gene transcription is governed by a hierarchical regulatory cascade that involves gene activation and gene repression. The σ<sup>E</sup> factor turns on a large regulon that includes the genes for GerR and SpoIIID. These DNA-binding proteins, in turn, block further transcription of many of the genes that had been activated by σ<sup>E</sup>. SpoIIID is also an activator, and it turns on genes required for the appearance of pro-σ<sup>K</sup>. The conversion of pro-σ<sup>K</sup> to mature σ<sup>K</sup> is governed by a signal emanating from the forespore as represented by the squiggle. Next, σ<sup>K</sup> activates the subsequent regulon in the cascade, which includes the gene for the DNA-binding protein GerE. Finally, GerE, which, like SpoIIID, is both an activator and a repressor, turns on the final regulon in the cascade while also repressing many of the genes that had been activated by σ<sup>K</sup>. The thickness of lines represents the relative abundance of genes activated (arrows) or repressed (lines ending in bars) by the indicated regulatory proteins.</p>
<p>(B) The regulatory circuit is composed of two coherent FFLs linked in series and three incoherent FFLs. In the first coherent FFL, σ<sup>E</sup> turns on the synthesis of SpoIIID, and both factors act together to switch on target genes, including genes involved in the appearance of σ<sup>K</sup>. Likewise, in the second coherent FFL, σ<sup>K</sup> directs the synthesis of GerE, and the two factors then act together to switch on target genes (X<sub>4</sub>). The σ<sup>E</sup> factor and SpoIIID also constitute an incoherent FFL in which SpoIIID acts as a repressor to downregulate the transcription of a subset of the genes (X<sub>2</sub>) that had been turned on by σ<sup>E</sup>. Similar incoherent FFLs are created by the actions of σ<sup>E</sup> and GerR (X<sub>1</sub>) and by σ<sup>K</sup> and GerE (X<sub>3</sub>), with GerR and GerE repressing genes that had been switched on by σ<sup>E</sup> and σ<sup>K</sup>, respectively. The AND symbols indicate that the FFLs operate by the logic of an AND gate in that the output (either gene activation or a pulse of gene expression) requires the action of both transcription factors in the FFL (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020328#pbio-0020328-Mangan1" target="_blank">Mangan and Alon 2003</a>). For example, σ<sup>K</sup> and GerE are both required for the activation of X<sub>4</sub> genes, whose induction is delayed compared to genes that are turned on by σ<sup>K</sup> alone. Similarly, both σ<sup>E</sup> and the delayed appearance of GerR are anticipated to create a pulse of transcription of X<sub>1</sub> genes.</p></div