Fast and Scriptable Molecular Graphics in Web Browsers without Java3D

Willighagen, Egon; Howard, Miguel

doi:10.1038/npre.2007.50.1

Cited by 23 publications

(20 citation statements)

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“…Protein structure figures were created using Jmol (http://www.jmol.org), PyMol (http://pymol.org), and MolMol (http://www-theor.ch.cam.ac.uk/IT/software/molmol.html ) [103]–[105]. Some PDB data parsing and protein sequence creation was performed using BioJava 3 (http://www.biojava.org) [106].…”

Section: Methodsmentioning

confidence: 99%

Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

et al. 2012

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Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function.

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Section: Methodsmentioning

confidence: 99%

Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

et al. 2012

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“…Analysis using Jmol software 29 revealed that Gln92 is in close proximity to Glu133 (8.6 Å ), Glu112 (10 Å ), Asp113 (12.7 Å ), and Glu109 (13 Å ). Thus, the formation of a Glu residue at position 92 might be expected to cause significant charge-charge repulsion and potentially to lead to a more open, unfolded tertiary structure.…”

Section: Discussionmentioning

confidence: 99%

Age‐dependent deamidation of glutamine residues in human γS crystallin: Deamidation and unstructured regions

2012

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Human aging is associated with the deterioration of long-lived proteins. Gradual cumulative modifications to the life-long proteins of the lens may ultimately be responsible for the pronounced alterations to the optical and physical properties that characterize lenses from older people. cS crystallin, a major human lens protein, is known to undergo several age-dependent changes. Using proteomic techniques, a site of deamidation involving glutamine 92 has been characterized and its time course established. The proportion of deamidation increased from birth to teen-age years and then plateaud. Deamidation at this site increased again in the eighth decade of life. There was no significant difference in the extent of deamidation between cataract and age-matched normal lenses. Gln92 is located in the linker region between the two domains, and the introduction of a negative charge at this site may alter the interaction between the two regions of the protein. Gln170, which is located in another unstructured part of cS crystallin, showed a similar deamidation profile to that of Gln92. As the other Gln residues in b-sheet regions of cS crystallin appear to remain as amides, modification of Gln92 and Gln170 thus conforms to a pattern whereby deamidation is localized to the unstructured regions of long-lived proteins.

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“…The electrostatic surface potentials were calculated by solving the linearized PoissoneBoltzmann equation (PBE) with the APBS package (version 1.3) [27]. 3D structures with surface potentials produced by APBS were visualized using Jmol viewer (version 12.0) [28]. The molecular hydrophobic and hydrophilic properties of the predicted models were calculated by the PLATINUM web-server based on the concept of empirical Molecular Hydrophobicity Potential [29].…”

Section: Protein 3d Structure Modelingmentioning

confidence: 99%

Protein domain repetition is enriched in Streptococcal cell-surface proteins

Lin

Hsu

Chang³

2012

Genomics

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Tandem repetition of domain in protein sequence occurs in all three domains of life. It creates protein diversity and adds functional complexity in organisms. In this work, we analyzed 52 streptococcal genomes and found 3748 proteins contained domain repeats. Proteins not harboring domain repeats are significantly enriched in cytoplasm, whereas proteins with domain repeats are significantly enriched in cytoplasmic membrane, cell wall and extracellular locations. Domain repetition occurs most frequently in S. pneumoniae and least in S. thermophilus and S. pyogenes. DUF1542 is the highest repeated domain in a single protein, followed by Rib, CW_binding_1, G5 and HemolysinCabind. 3D structures of 24 repeat-containing proteins were predicted to investigate the structural and functional effect of domain repetition. Several repeat-containing streptococcal cell surface proteins are known to be virulence-associated. Surface-associated tandem domain-containing proteins without experimental functional characterization may be potentially involved in the pathogenesis of streptococci and deserve further investigation.

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Fast and Scriptable Molecular Graphics in Web Browsers without Java3D

Cited by 23 publications

References 0 publications

Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

Age‐dependent deamidation of glutamine residues in human γS crystallin: Deamidation and unstructured regions

Protein domain repetition is enriched in Streptococcal cell-surface proteins

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