Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes

A largely unsolved problem in computational biochemistry is the accurate prediction of binding affinities of small ligands to protein receptors. We present a detailed analysis of the systematic and random errors present in computational methods through the use of error probability density functions, specifically for computed interaction energies between chemical fragments comprising a protein-ligand complex. An HIV-II protease crystal structure with a bound ligand (indinavir) was chosen as a model protein-ligand complex. The complex was decomposed into twenty-one (21) interacting fragment pairs, which were studied using a number of computational methods. The chemically accurate complete basis set coupled cluster theory (CCSD(T)/CBS) interaction energies were used as reference values to generate our error estimates. In our analysis we observed significant systematic and random errors in most methods, which was surprising especially for parameterized classical and semiempirical quantum mechanical calculations. After propagating these fragment-based error estimates over the entire protein-ligand complex, our total error estimates for many methods are large compared to the experimentally determined free energy of binding. Thus, we conclude that statistical error analysis is a necessary addition to any scoring function attempting to produce reliable binding affinity predictions.     

Studying Systematic Errors on Estimation Decision, Detection, and Quantification Limit on Micro-TLC

The decision limit (CCα), capability of detection (CCβ) and quantification limit (QL) are importance performance characteristics in method validation. The TLC-Scanner 3 from Camag provides the possibility to choose the slit dimension of light to determine the peak chromatogram of a substance. The influence of the slit dimension for determination of CCα, CCβ and QL of paracetamol has been carried out. Paracetamol was spotted onto plates of AL-TLC Si G 60 F254 by linomat 4 in the range of 50–400 ng/spot and 10–400 ng/band, then on twin chambers eluted with TAEA (toluene:acetone-ethanol:conc.ammonia, 45 + 45 + 7 + 3 v/v) for 45 mm. Eluted spots were scanned in different slit dimensions at 248 nm. The CCα, CCβ and QL of paracetamol were estimated through the linear regression (LRM) and signal-to-noise (S/N) methods. Slit lengths between 50 and 133 % of the band width of the spots, and with the noise factor of the slit under 2.6, produced good precision measurements of TLC-densitometry between plates, while slit lengths between 50 and 83 % of the band width of the spots introduced a higher sensitivity response of the detector. The estimated CCα, CCβ and QL were determined by how the data were collected, the analytical optical setting, and the usage method for the estimation of both validation parameters.     

湛江港湾海产动物污染残毒的测定与评价

介绍了用原子吸收分光光度法等测定湛江港湾海产动物的污染残毒水平，并对其残毒水平及海产品质量进行了评价。     

Measurement of Gamma-Dose Caused by Built in Coal Slags with Elevated 226Ra Concentration, and the Modelling of Shielding

Slags, derived from coal mined in the neighbourhood of the town Tatabánya in Hungary, have been used as filling and insulating material for buildings of houses, block of flats, schools and kindergartens. The slag samples come from here have elevated concentrations of ²²⁶Ra, (range of 850–2400 Bq·kg^–1). Therefore, the external gamma dose rates at 1 m height were about four times higher than the world average. It has been found, based on the modelling, that the dose rate could be decreased with 70–80% using an appropriate thickness of concrete or barite-concrete layers.     

Errors,PGAA, and metrology

Analytical chemists are scientific scavengers, using any available physical phenomenon to determine the composition of materials. Accuracy, unlike mere reproducibility, depends on understanding the measurement process, most usefully by stressing it until it bends. The use of neutron capture gamma rays for analysis involves some issues not encountered in conventional neutron activation analysis which, when understood, extend the utility and reinforce the value of nuclear methods of elemental analysis. These methods are being increasingly recognized as tools for SI-traceable metrology.     

生物矿化过程及其模拟

国家自然科学基金委员会化学科学部于１９９９年３月１５—１６日在北京召开了“生物矿化过程及其模拟”学术讨论会。从事与生物矿化有关研究的化学、材料科学、古生物学的专家２０余人参加了会议。本次讨论会突出创新意识,与会专家联系自己的学科和各自的研究工作,从不...     

Estimation and Comparison of Pore Charge on Titania and Zirconia Membranes Prepared by Sol-Gel Route Using Zeta Potential Measurement

An attempt has been made to synthesize ceramic titania and zirconia membranes by sol-gel process by filtering respective viscous colloidal sol through microporous alumina support and gelling followed by sintering at 400°C and 470°C respectively. The static charge on the pores of the so formed membranes and the pore size distribution determine the applicability in filtering colloidal solution. The mean pore size from SEM were found to be 0.65 m and 0.54 m for titania and zirconia membranes respectively with 1.47 × 10⁷/cm² as pore density for both. The filtration characteristics during membrane layer formation showed that the membrane layer formation started after 35 minutes in the case of titania membrane and 40 minutes in the case of zirconia membrane. From the gravimetric estimation of water content of the membranes the thickness of the membrane was found out to be 3 m and the porosity was found out to be 0.30 for both the cases. The particle charge density was estimated from the zeta potential and the particle size. The pore charge density was estimated from the particle charge density, pore density, pore diameter and the thickness of the membrane layer. The membrane pore charge density was found to vary between 3 to –1 Coulombs/cm² in the case of titania membrane and 7 to –0.5 Coulombs/cm² in the case of zirconia membrane in the pH range 1–12.     

Measurement of particle size distribution in the discrete phase of high-impact polystyrene. I. Errors in direct coulter counter techniques

The published Coulter Counter method for measuring particle size distribution of the discrete phase in rubber-modified polystyrene is shown to be subject to serious limitations, especially when the data generated are used to compute discrete phase volume fractions. The source of error is time-dependent swelling of the particles in DMF which is used to isolate them from the polystyrene matrix for the counting operation.     

Measurement of Large Dipolar Couplings of a Liquid Crystal with Terminal Phenyl Rings and Estimation of the Order Parameters

NMR spectroscopy is a powerful means of studying liquid‐crystalline systems at atomic resolutions. Of the many parameters that can provide information on the dynamics and order of the systems, ¹H–¹³C dipolar couplings are an important means of obtaining such information. Depending on the details of the molecular structure and the magnitude of the order parameters, the dipolar couplings can vary over a wide range of values. Thus the method employed to estimate the dipolar couplings should be capable of estimating both large and small dipolar couplings at the same time. For this purpose, we consider here a two‐dimensional NMR experiment that works similar to the insensitive nuclei enhanced by polarization transfer (INEPT) experiment in solution. With the incorporation of a modification proposed earlier for experiments with low radio frequency power, the scheme is observed to enable a wide range of dipolar couplings to be estimated at the same time. We utilized this approach to obtain dipolar couplings in a liquid crystal with phenyl rings attached to either end of the molecule, and estimated its local order parameters.     

人物形象的塑造—论汪曾祺文学创作中的鲁迅因子

汪曾祺的文学创作深受鲁迅的影响。因汪曾祺十分重视文学创作的语言,又多次在文论中言及鲁迅的小说语言,故学界多从语言层面考察鲁迅对汪曾祺的影响。但是,人物形象的塑造是鲁迅影响汪曾祺文学创作更为深刻的因子。这种影响既有僧侣形象以及古人形象重塑的因素,也有刻画人物形象的文学理念以及创作技法的因素。在人物塑造上,汪曾祺深受鲁迅的影响毋庸置疑,但又是有选择性的借鉴。这种创造性的借鉴无疑为当代文坛提供了有益的文学经验。     

应当正视教材练习题上的2处硬伤

指出了人教版《化学1》教材上的2处硬伤,常温常压下硫酸铜溶液浓度不可能达到2 mol/L,实验时更不可能给学生1试管NO2。实验发现,通常情况下,将1试管NO2倒扣在水中,待液面基本稳定时,水位上升远远不止2/3试管。     

Correction of Errors during Protein Synthesis

Quality control : The incorporation of a wrong amino acid into a growing polypeptide chain induces a correction step in which the release factor (RF1) hydrolyzes the peptide from the incorrectly matched peptidyl‐tRNA (see picture). The nascent erroneous polypeptide is released from the ribosome and degraded.

     

Modelling of icosahedral viruses

Theoretical and simulation investigations of viruses attaining icosahedral shape based on molecular models have recently become an exciting and rapidly growing research area. We discuss recent studies addressing the packing of the genome inside the capsid, thermodynamics, and the self-assembly of capsids. Special attention is given to the different packing of double-stranded and single-stranded polynucleotides in the viral capsid and its consequences.     

Methods of Detecting and/or Reducing Systematic Errors in Quantitative Planar Chromatography. Part 3. Evaluation and Calibration Errors

JPC – Journal of Planar Chromatography – Modern TLC -