An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering...An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large- and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments.展开更多
Early disease detection is extremely important in the treatment and prognosis of many diseases, especially cancer. Often, proteomic fingerprints and a pattern recognition algorithm are used to classify the pathologica...Early disease detection is extremely important in the treatment and prognosis of many diseases, especially cancer. Often, proteomic fingerprints and a pattern recognition algorithm are used to classify the pathological condition of a given individual. It has been argued that accurate classification of the existing data implies an underlying biological significance. Two fingerprint-based classifiers, decision tree and medoid classification algorithm, and a biomarker-based classifier were examined using a published dataset of mass spectral peaks from 81 healthy individuals and 78 individuals with benign prostate hyperplasia (BPH). For all three methods, classifiers were constructed using the original data and the data after permuting the labels of the samples (BPH and healthy). The fingerprint-based classifiers produced accurate results for the original data, though the peaks used in a given classifier depended upon which samples were placed in the training set. Accurate results were also obtained for the dataset with permuted labels. In contrast, only three unique peaks were identified as putative biomarkers, producing a small number of reasonably accurate biomarker-based classifiers. The dataset with permuted labels was poorly classified. Since fingerprint-based classifiers accurately classified the dataset with permuted labels, the argument for biological significance from a fingerprint-based classifier must be questioned.展开更多
文摘An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large- and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments.
文摘Early disease detection is extremely important in the treatment and prognosis of many diseases, especially cancer. Often, proteomic fingerprints and a pattern recognition algorithm are used to classify the pathological condition of a given individual. It has been argued that accurate classification of the existing data implies an underlying biological significance. Two fingerprint-based classifiers, decision tree and medoid classification algorithm, and a biomarker-based classifier were examined using a published dataset of mass spectral peaks from 81 healthy individuals and 78 individuals with benign prostate hyperplasia (BPH). For all three methods, classifiers were constructed using the original data and the data after permuting the labels of the samples (BPH and healthy). The fingerprint-based classifiers produced accurate results for the original data, though the peaks used in a given classifier depended upon which samples were placed in the training set. Accurate results were also obtained for the dataset with permuted labels. In contrast, only three unique peaks were identified as putative biomarkers, producing a small number of reasonably accurate biomarker-based classifiers. The dataset with permuted labels was poorly classified. Since fingerprint-based classifiers accurately classified the dataset with permuted labels, the argument for biological significance from a fingerprint-based classifier must be questioned.
