CHARMMing: A New, Flexible Web Portal for CHARMM

Miller, Benjamin; Singh, Rishi P.; Klauda, Jeffery B.; Hodošček, Milan; Brooks, Bernard R.; Woodcock, H. Lee

doi:10.1021/ci800133b

Cited by 127 publications

(127 citation statements)

References 39 publications

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“…Complementing Q-CHEM/CHARMM support for QM/MM dielectric approaches (see also QM/MM/PCM below), the solvent macromolecule boundary potential method has also been interfaced to Q-CHEM [298,299]. Last, but not least, a user-friendly Web interface that facilitates the graphical set-up of QM/MM calculations (i.e., Q-CHEM/CHARMM) was also developed [300]. It is anticipated that this will receive significant enhancements in the near future and tie closely into IQMOL, which is discussed in Section 9.…”

Section: Qm/mm and Fragment Methodsmentioning

confidence: 99%

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Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Shao¹,

Gan²,

Epifanovsky³

et al. 2014

Molecular Physics

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2,746

2,077

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A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and openshell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr 2 dimer, exploring zeolitecatalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.Keywords quantum chemistry, software, electronic structure theory, density functional theory, electron correlation, computational modelling, Q-Chem Disciplines Chemistry CommentsThis article is from Molecular Physics: An International Journal at the Interface Between Chemistry and Physics 113 (2015): 184, doi:10.1080/00268976.2014. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. Authors 185A summary of the technical advances that are incorporated in the fourth major release of the Q-CHEM quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly corre...

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Section: Qm/mm and Fragment Methodsmentioning

confidence: 99%

“…Q-CHEM is also interfaced with a variety of other public domain user interfaces, including CHARMMing [300] Avogadro [416], Molden [417], and WebMO [418].…”

Section: Other Interfacesmentioning

confidence: 99%

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Shao¹,

Gan²,

Epifanovsky³

et al. 2014

Molecular Physics

Self Cite

2,746

2,077

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“…The simulations were extended up to 50 ns, preceded by an equilibration phase of 1 ns. The computational setup used here can be configured automatically (29) through the Web interface at http://www .charmming.org. Residues 230 to 234 and 283 to 287 of hPRLR were not resolved in the X-ray structure.…”

Section: Methodsmentioning

confidence: 99%

Intramolecular Disulfide Bonds of the Prolactin Receptor Short Form Are Required for Its Inhibitory Action on the Function of the Long Form of the Receptor

Xie

Hassan

Qazi

et al. 2009

Molecular and Cellular Biology

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The short form (S1b) of the prolactin receptor (PRLR) silences prolactin-induced activation of gene transcription by the PRLR long form (LF). The functional and structural contributions of two intramolecular disulfide (S-S) bonds within the extracellular subdomain 1 (D1) of S1b to its inhibitory function on the LF were investigated. Mutagenesis of the paired cysteines eliminated the inhibitory action of S1b. The expression of the mutated S1b (S1bx) on the cell surface was not affected, indicating native-like folding of the receptor. The constitutive JAK2 phosphorylation observed in S1b was not present in cells expressing S1bx, and JAK2 association was disrupted. BRET 50 (BRET 50 represents the relative affinity as acceptor/donor ratio required to reach half-maximal BRET [bioluminescence resonance energy transfer] values) showed decreased LF/S1bx heterodimeric-association and increased affinity in S1bx homodimerization, thus favoring LF homodimerization and prolactin-induced signaling. Computer modeling based on the PRLR crystal structure showed that minor changes in the tertiary structure of D1 upon S-S bond disruption propagated to the quaternary structure of the homodimer, affecting the dimerization interface. These changes explain the higher homodimerization affinity of S1bx and provide a structural basis for its lack of inhibitory function. The PRLR conformation as stabilized by S-S bonds is required for the inhibitory action of S1b on prolactin-induced LF-mediated function and JAK2 association.The prolactin receptor (PRLR) belongs to the class I cytokine receptor superfamily (4, 5). It binds the pituitary hormone prolactin (PRL) with high affinity and triggers intracellular responses that participate in diverse biological functions in target tissues, including the mammary gland, organs of the reproductive system, the central nervous system, pituitary, and adrenal. At least nine variants are generated by alternative splicing of the human PRLR (hPRLR) gene (16-18, 21, 35); they differ in the lengths and compositions of their cytoplasmic domains and/or extracellular (EC) domains (http://atlasgeneticsoncology.org/Genes /PRLRID42891ch5p14.html). The full-length receptor, or long form (LF), is composed of a ligand binding EC domain, a single transmembrane domain, and a cytoplasmic domain required for signal transduction (5, 20). PRL acts through the LF to stimulate cell proliferation and differentiation. The short forms (SFs) of the receptor, S1a and S1b, are derived from alternative splicing of exons 10 and 11 and contain unique cytoplasmic sequences (16). S1a is a 376-amino-acid (aa) receptor that contains partial exon 10 sequences and a unique 39-aa C terminus derived from exon 11. S1b is a 288-aa variant that lacks the entire exon 10 and contains 3 aa derived from exon 11 at the C terminus. Unlike the LF, neither of the SF receptors can mediate activation of the ␤-casein gene promoter induced by PRL, and both SFs are inhibitory of the transcriptional activation induced by PRL through the LF (16). S1b is more ...

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“…To generate the wild type model the aspartate at position 45 was converted to an asparagine, asparagine at position 47 was converted to an aspartate, and the methionine at position 61 was converted to an arginine. Both the native and modified model were subjected to energy minimization using the macromolecular modeling package CHARMMing tool in the default settings (19). The structural implications were analyzed using MacPyMOL.…”

Section: Modeling Of the Wild Type And Variant Amcase Isoformsmentioning

confidence: 99%

Differential Enzymatic Activity of Common Haplotypic Versions of the Human Acidic Mammalian Chitinase Protein

Seibold

Reese

Choudhry

et al. 2009

Journal of Biological Chemistry

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Mouse models have shown the importance of acidic mammalian chitinase activity in settings of chitin exposure and allergic inflammation. However, little is known regarding genetic regulation of AMCase enzymatic activity in human allergic diseases. Resequencing the AMCase gene exons we identified 8 non-synonymous single nucleotide polymorphisms including three novel variants (A290G, G296A, G339T) near the gene area coding for the enzyme active site, all in linkage disequilibrium. AMCase protein isoforms, encoded by two gene-wide haplotypes, and differentiated by these three single nucleotide polymorphisms, were recombinantly expressed and purified. Biochemical analysis revealed the isoform encoded by the variant haplotype displayed a distinct pH profile exhibiting greater retention of chitinase activity at acidic and basic pH values. Determination of absolute kinetic activity found the variant isoform encoded by the variant haplotype was 4-, 2.5-, and 10-fold more active than the wild type AMCase isoform at pH 2.2, 4.6, and 7.0, respectively. Modeling of the AMCase isoforms revealed positional changes in amino acids critical for both pH specificity and substrate binding. Genetic association analyses of AMCase haplotypes for asthma revealed significant protective associations between the variant haplotype in several asthma cohorts. The structural, kinetic, and genetic data regarding the AMCase isoforms are consistent with the Th2-priming effects of environmental chitin and a role for AMCase in negatively regulating this stimulus.

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CHARMMing: A New, Flexible Web Portal for CHARMM

Cited by 127 publications

References 39 publications

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Intramolecular Disulfide Bonds of the Prolactin Receptor Short Form Are Required for Its Inhibitory Action on the Function of the Long Form of the Receptor

Differential Enzymatic Activity of Common Haplotypic Versions of the Human Acidic Mammalian Chitinase Protein

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