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Biomedical subjects

B C Sanctuary

Publications and source records attributed to B C Sanctuary.

7 recordsLinked to original sources
PubMed1998

Spectral parameter estimation by an iterative quadratic maximum likelihood method.

An iterative quadratic maximum likelihood (IQML) method is applied to spectral parameter estimation of 1D NMR data. A careful comparison of the linear prediction (LP) method based on the singular value decomposition, the total least squares (TLS) method, and IQML has clearly demonstrated that IQML is superior to both the LP and TLS methods in terms of the accuracy and bias of the estimation. The superiority of the IQML method lies in the fact that constraints on the NMR signal can easily be incorporated into the iterative process. The iterative quadratic maximum likelihood method can be used to analyze NMR data directly or to provide a starting point for further data refinement.

Algorithms↗
PubMed1991

Alkalosis monitored by 31P NMR in a human glioma cell line exposed to the anti-tumor drug 1,3-bis(2-chloroethyl)-1-nitrosourea.

A transient alkalosis of similar magnitude to that observed in vivo has been observed using 31P NMR and 2-deoxy-D-glucose-6-phosphate as a pH marker in a human glioma cell line, SKI-1, with demonstrated sensitivity to 1,3-bis(2-chloroethyl)-1-nitrosourea. At an effective dose of 5 +/- 1 x 10 micrograms/ml, an increase of 0.13 +/- 0.05 pH units was observed within 4 +/- 1 x 10 min of introducing the drug into the perfusion chamber. Although the in vitro response is of a time course much faster than that in vivo, these results suggest that this immediate pH change could be an indicator of the cytotoxic action of the drug.

Carmustine↗
PubMed1991

1H NMR characterization of normal human cerebrospinal fluid and the detection of methylmalonic acid in a vitamin B12 deficient patient.

1H NMR was used to analyze human cerebrospinal fluid (CSF) from a group of neurological disease controls and from a vitamin B12 deficient patient. The spectra were acquired at either 7.06 or 9.40 T at ambient temperature with CSF freeze dried and reconstituted in 2H2O. 3-Trimethylsilyl propionate was used as an internal chemical shift and concentration reference. All of the CSF samples showed peaks for lactate, L-alanine, acetate, glutamine, citrate, creatine/creatinine and sugar resonances. There was good agreement between the metabolite concentrations as determined by NMR with those obtained using conventional chemical methods. 1D and 2D 1H NMR techniques along with J-coupling and T1 analysis were used to confirm the peak assignments. Methylmalonic acid could be detected and quantitated (ca 150 microM) in the CSF from the vitamin B12 deficient patient.

Adult↗
PubMedDate not supplied

Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory.

The novel methodology for protein 2D NMR assignment presented in this paper is based upon protein spin coupling graph theory analysis, fuzzy graph pattern recognition, and tree searching. The method required to formalize the whole assignment procedure into a logical system which can be properly processed by computer software is also discussed. Solutions for peak overlaps, spin coupling network overlaps, and details related to the automated assignment of BPTI are reported as well.

Algorithms↗
PubMedDate not supplied

Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.

A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid coupling patterns. Both chemical shift and topologically likeness are considered. The mapping algorithm uses the amino acid type information to direct detected polypeptides to proper position onto protein primary sequence. The assignment protocol can be applied to spin systems generated by many different approaches. We designed a few computer programs to derive a protein's backbone and side chain spin systems using heteronuclear 3D NMR. The results was then input to the sequential assignment protocol. All of the algorithms were tested on NMR data of a 90-residue N-domain of chicken skeletal troponin-C.

Algorithms↗
PubMedDate not supplied

Using neural network predicted secondary structure information in automatic protein NMR assignment.

In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of chemical shift distributions of the 20 amino acid types, fuzzy mathematics, and pattern recognition theory, the spin coupling topological graphs are mapped onto specific amino acid residues. In this work, we investigated the feasibility of using secondary structure information of proteins as predicted by neural networks in the automated NMR assignment. As the 1H and 13C chemical shifts of proteins are known to correlate to their secondary structures, secondary structure information is useful in improving the amino acid recognition. In this study, the secondary structures of proteins predicted by the PHD protein server and our own trained neural networks are used in the amino acid type recognition. The results show that the predicted secondary structure information can help to improve the accuracy of the amino acid recognition.

Algorithms↗