Journal of the Acoustical Society of America, Sep 1, 1987
BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication st... more BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication steps which are economically expen-This invention relates to musical instruments and srve^ 0 achieve, more specifically to digitally controlled electronic in-In a typical example of a filter technique, a wavestruments and methods for generating musical sound. 15 shape memory provides digital samples of one cycle of Digitally controlled methods of generating musical a waveshape to a loop circuit which includes a filter and ...
This paper makes a quantitative comparison of different methods, called regularizers, for estimat... more This paper makes a quantitative comparison of different methods, called regularizers, for estimating the distribution of amino acids in a specific context, given a very small sample of amino acids from that distribution. The regularizers considered here are zero-offsets, pseudocounts, substitution matrices (with several variants), and Dirichlet mixture regularizers. Each regularizer is evaluated based on how well it estimates the distributions of the columns of a multiple alignment--specifically, the expected encoding cost per amino acid using the regularizer and all possible samples from each column. In general, pseudocounts give the lowest encoding costs for samples of size zero, substitution matrices give the lowest encoding costs for samples of size one, and Dirichlet mixtures give the lowest for larger samples. One of the substitution matrix variants, which added pseudocounts and scaled counts, does almost as well as the best known Dirichlet mixtures, but with a lower computation cost.
Protein Engineering Design & Selection, Oct 24, 2005
This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into ... more This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, a-protons, b-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, a-protons, b-protons in a-helices, antiparallel b-sheets and parallel b-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.
This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for repre... more This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for representing and manipulating Boolean functions. Two-cuts are de ned for binary decision diagrams, and a relationship is exhibited between general if-then-else expressions and the two-cuts of a BDD for the same function. An algorithm for computing all two-cuts of a BDD in O(n 2 ) time is given. A new canonical form for if-then-else dags, analogous to Bryant's canonical form for BDDs, is introduced. The canonical form is based on representing the lowest non-trivial two-cut in the corresponding BDD, while Bryant's canonical form represents the highest two-cut. Expressions in Bryant's canonical form or in the new canonical form are shown to be prime and irredundant. Some applications of if-then-else dags to multi-level logic minimization are given, and the Printform transformations for reducing the complexity of if-then-else dags are presented. This research was partially supported by an IBM Faculty Development Award and by NSF grant DCR-8503262.
Prediction of protein structures continues to be a difficult problem, particularly when there are... more Prediction of protein structures continues to be a difficult problem, particularly when there are no solved structures for homologous proteins to use as templates. Local structure prediction (secondary structure and burial) is fairly reliable, but does not provide enough information to produce complete three-dimensional structures. Residueresidue contact prediction, though still not highly reliable, may provide useful guide for assembling local structure prediction into full tertiary prediction. We develop a neural network which is applied to pairs of residue positions and outputs a probability of contact between the positions. One of the neural net inputs is a novel statistic for detecting correlated mutations: the statistical significance of the mutual information between the corresponding columns of a multiple sequence alignment. This statistic, combined with a second statistic based on the propensity of two amino acid types being in contact, results in a simple neural network that is a good predictor of contacts. Adding more features from amino-acid distributions and local structure predictions, the final neural network predicts contacts better than other submitted contact predictions at CASP7, including contact predictions derived from fragment-based tertiary models on freemodeling domains. It is still not known if contact predictions can improve tertiary models on free-modeling domains.
The SAM-T08 web server is a protein structure prediction server that provides several useful inte... more The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue-residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http:// compbio.soe.ucsc.edu/SAM_T08/T08-query.html
Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be i... more Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. The rugose variant forms corrugated colonies, exhibits increased levels of resistance to osmotic, acid, and oxidative stresses, and has an enhanced capacity to form biofilms. Many of these phenotypes are mediated in part by increased production of an exopolysaccharide termed VPS. In this study, we compared total protein profiles of the smooth and rugose variants using two-dimensional gel electrophoresis and identified one protein that is present at a higher level in the rugose variant. A mutation in the gene encoding this protein, which does not have any known homologs in the protein databases, causes cells to form biofilms that are more fragile and sensitive to sodium dodecyl sulfate than wild-type biofilms. The results indicate that the gene, termed rbmA (rugosity and biofilm structure modulator A), is required for rugose colony formation and biofilm structure integrity in V. cholerae. Transcription of rbmA is positively regulated by the response regulator VpsR but not VpsT.
Journal of the Acoustical Society of America, Sep 1, 1987
BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication st... more BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication steps which are economically expen-This invention relates to musical instruments and srve^ 0 achieve, more specifically to digitally controlled electronic in-In a typical example of a filter technique, a wavestruments and methods for generating musical sound. 15 shape memory provides digital samples of one cycle of Digitally controlled methods of generating musical a waveshape to a loop circuit which includes a filter and ...
This paper makes a quantitative comparison of different methods, called regularizers, for estimat... more This paper makes a quantitative comparison of different methods, called regularizers, for estimating the distribution of amino acids in a specific context, given a very small sample of amino acids from that distribution. The regularizers considered here are zero-offsets, pseudocounts, substitution matrices (with several variants), and Dirichlet mixture regularizers. Each regularizer is evaluated based on how well it estimates the distributions of the columns of a multiple alignment--specifically, the expected encoding cost per amino acid using the regularizer and all possible samples from each column. In general, pseudocounts give the lowest encoding costs for samples of size zero, substitution matrices give the lowest encoding costs for samples of size one, and Dirichlet mixtures give the lowest for larger samples. One of the substitution matrix variants, which added pseudocounts and scaled counts, does almost as well as the best known Dirichlet mixtures, but with a lower computation cost.
Protein Engineering Design & Selection, Oct 24, 2005
This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into ... more This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, a-protons, b-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, a-protons, b-protons in a-helices, antiparallel b-sheets and parallel b-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.
This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for repre... more This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for representing and manipulating Boolean functions. Two-cuts are de ned for binary decision diagrams, and a relationship is exhibited between general if-then-else expressions and the two-cuts of a BDD for the same function. An algorithm for computing all two-cuts of a BDD in O(n 2 ) time is given. A new canonical form for if-then-else dags, analogous to Bryant's canonical form for BDDs, is introduced. The canonical form is based on representing the lowest non-trivial two-cut in the corresponding BDD, while Bryant's canonical form represents the highest two-cut. Expressions in Bryant's canonical form or in the new canonical form are shown to be prime and irredundant. Some applications of if-then-else dags to multi-level logic minimization are given, and the Printform transformations for reducing the complexity of if-then-else dags are presented. This research was partially supported by an IBM Faculty Development Award and by NSF grant DCR-8503262.
Prediction of protein structures continues to be a difficult problem, particularly when there are... more Prediction of protein structures continues to be a difficult problem, particularly when there are no solved structures for homologous proteins to use as templates. Local structure prediction (secondary structure and burial) is fairly reliable, but does not provide enough information to produce complete three-dimensional structures. Residueresidue contact prediction, though still not highly reliable, may provide useful guide for assembling local structure prediction into full tertiary prediction. We develop a neural network which is applied to pairs of residue positions and outputs a probability of contact between the positions. One of the neural net inputs is a novel statistic for detecting correlated mutations: the statistical significance of the mutual information between the corresponding columns of a multiple sequence alignment. This statistic, combined with a second statistic based on the propensity of two amino acid types being in contact, results in a simple neural network that is a good predictor of contacts. Adding more features from amino-acid distributions and local structure predictions, the final neural network predicts contacts better than other submitted contact predictions at CASP7, including contact predictions derived from fragment-based tertiary models on freemodeling domains. It is still not known if contact predictions can improve tertiary models on free-modeling domains.
The SAM-T08 web server is a protein structure prediction server that provides several useful inte... more The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue-residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http:// compbio.soe.ucsc.edu/SAM_T08/T08-query.html
Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be i... more Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. The rugose variant forms corrugated colonies, exhibits increased levels of resistance to osmotic, acid, and oxidative stresses, and has an enhanced capacity to form biofilms. Many of these phenotypes are mediated in part by increased production of an exopolysaccharide termed VPS. In this study, we compared total protein profiles of the smooth and rugose variants using two-dimensional gel electrophoresis and identified one protein that is present at a higher level in the rugose variant. A mutation in the gene encoding this protein, which does not have any known homologs in the protein databases, causes cells to form biofilms that are more fragile and sensitive to sodium dodecyl sulfate than wild-type biofilms. The results indicate that the gene, termed rbmA (rugosity and biofilm structure modulator A), is required for rugose colony formation and biofilm structure integrity in V. cholerae. Transcription of rbmA is positively regulated by the response regulator VpsR but not VpsT.
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