Average Root Mean Square Deviation Research Articles

Assessment of straight, zigzag, S-shape, and airfoil PCHEs for intermediate heat exchangers of HTGRs and SFRs

A promising candidate for the intermediate heat exchanger (IHX) in high temperature gas-cooled reactors (HTGRs) and sodium-cooled fast reactors (SFRs) is a printed circuit heat exchanger (PCHE) due to its high effectiveness and compactness. We developed the thermal–hydraulic correlations for an airfoil PCHE by three-dimensional computational fluid dynamics (3D-CFD) analysis, which are applicable over the range of Reynolds number from 0 to 150,000, including helium in laminar region and CO2 in turbulent region. Proposed Fanning factor correlation for the entire range showed the normalized root mean square deviation (NRMSD) as 2.52%. NRMSDs for two Nusselt number models for each flow region were calculated as 4.66% and 0.82%. We compared the total cost considering material and operation cost for the IHXs in HTGRs and SFRs with 4 types of PCHEs, which are straight, zigzag, S-shape, and airfoil PCHEs. For the IHXs of pebble bed modular reactor (PBMR) operating in the laminar region, the zigzag PCHE is the best option because of its lowest pressure drop and relatively high heat transfer area. The straight PCHE for the IHXs of Kalimer-600 is definitely the best option due to its much lower pressure drop, which is one reactor type of the SFRs operating in the turbulent region.

Model Based Inversion for Deriving Maps of Histological Parameters Characteristic of Cancer From Ex-Vivo Multispectral Images of the Colon

A model-based inversion method was used to obtain quantitative estimates of histological parameters from multispectral images of the colon and to examine their potential for discriminating between normal and pathological tissues. Pixel-wise estimates of the mucosal blood volume fraction, density of the scattering particles and thickness were derived using a two-stage method. In the first (forward) stage reflectance spectra corresponding to given instances of the parameter values were computed using Monte Carlo simulation of photon propagation through a multi-layered tissue. In the second (inversion) stage the parameter values were obtained via optimization using an iterated conditional modes algorithm based on Discrete Markov Random Fields. The method was validated on computer generated data contaminated with noise giving a mean normalized root mean square deviation (NRMSD) of 2.04. Validation on ex vivo images demonstrated that parametric maps show gross correspondence with histological features of mucosa characteristic of cancerous, precancerous and noncancerous colon lesions. The key signs of abnormality were shown to be the increase in the blood volume fraction and decrease in the density of scattering particles.

Structure and dynamic studies of lunatic, manic and radical fringe

O-Fucosylpeptide-3-beta-N-acetylglucosaminyltransferase (fringe) belongs to the family of glycosyltransferases. The modulator fringe participates in Notch signaling pathway. Various studies have shown that this modulator is involved in many developmental processes. The mutation or overexpression of fringe can lead to various diseases including cancer. Lunatic fringe (Lfng), manic fringe (Mfng) and radical fringe (Rfng), the paralogues of fringe, have not yet been studied at any level of computational biological research. The work accomplished in this study has been a step forward towards cutting edge research in the field of computational biology. Homology modeling and molecular dynamics simulation have been employed in order to study different structural, theoretical and dynamical properties of the fringe protein family. The 3D structures of fringe protein family which have not been reported previously in any of the structural database have been predicted by utilizing MODELLER tool. Structures were analyzed and validated through different structural and physicochemical characterization tools. Molecular dynamics simulation (MD simulation) has been employed on all three paralogues—Lfng, Mfng and Rfng—to investigate the protein dynamics of the fringe family at the atomic level reaching till the total production run of 15 ns. Time dependent behavior of protein on different time scales has been noticed through root mean square deviation (RMSD) and root mean square fluctuation (RMSF). The average RMSD for Lfng, Mfng and Rfng calculated was 3.07, 2.82 and 3.35Å, respectively, for the production run of 5ns each, depicting the stable structural dynamics of protein models. RMSD, RMSF, β factor and radius of gyration graphs showed the similar pattern of protein dynamics throughout the production run of 5ns each for Lfng, Mfng and Rfng. The DxD (aspartate any residue aspartate) motif, a hallmark active site of glycosyltransferases, remained well stabilized throughout the simulation run of fringe glycosyltransferase. This study is significantly important to interpret theoretical and dynamical behavior of the fringe protein family that also infers the conservation of similar dynamic pattern among same family of proteins which further demonstrates the sequence to dynamic similarity of proteins.

Automatic Estimation of Artemia Hatching Rate Using an Object Discrimination Method

Digital image processing is a process to analyze a large volume of information on digital images. In this study, Artemia hatching rate was measured by automatically classifying and counting cysts and larvae based on color imaging data from cyst hatching experiments using an image processing technique. The Artemia hatching rate estimation consists of a series of processes; a step to convert the scanned image data to a binary image data, a process to detect objects and to extract their shape information in the converted image data, an analysis step to choose an optimal discriminant function, and a step to recognize and classify the objects using the function. The function to classify Artemia cysts and larvae is optimally estimated based on the classification performance using the areas and the plan-form factors of the detected objects. The hatching rate using the image data obtained under the different experimental conditions was estimated in the range of 34-48%. It was shown that the maximum difference is about 19.7% and the average root-mean squared difference is about 10.9% as the difference between the results using an automatic counting (this study) and a manual counting were compared. This technique can be applied to biological specimen analysis using similar imaging information.

Use of weighted Fourier linear combiner filters to estimate lower trunk 3D orientation from gyroscope sensors data

BackgroundThe present study aimed at devising a data processing procedure that provides an optimal estimation of the 3-D instantaneous orientation of an inertial measurement unit (IMU). This result is usually obtained by fusing the data measured with accelerometers, gyroscopes, and magnetometers. Nevertheless, issues related to compensation of integration errors and high sensitivity of these devices to magnetic disturbances call for different solutions. In this study, a method based on the use of gyroscope data only is presented, which uses a Weighted Fourier Linear Combiner adaptive filter to perform a drift-free estimate of the 3D orientation of an IMU located on the lower trunk during walking.MethodsA tuning of the algorithm parameters and a sensitivity analysis to its initial conditions was performed using treadmill walking data from 3 healthy subjects. The accuracy of the method was then assessed using data collected from 15 young healthy subjects during treadmill walking at variable speeds and comparing the pitch, roll, and yaw angles estimated from the gyroscopes data to those obtained with a stereophotogrammetric system. Root mean square (RMS) difference and correlation coefficients (r) were used for this purpose.ResultsAn optimal set of values of the algorithm parameters was established. At all the observed speeds, and also in all the various sub-phases, the investigated angles were all estimated to within an average RMS difference of less than 1.2 deg and an average r greater than 0.90.ConclusionsThis study proved the effectiveness of the Weighted Fourier Linear Combiner method in accurately reconstructing the 3D orientation of an IMU located on the lower trunk of a subject during treadmill walking. This method is expected to also perform satisfactorily for overground walking data and to be applicable also to other “quasi-periodic” tasks, such as squatting, rowing, running, or swimming.

Using Optical Coherence Tomography to Assess Corneoscleral Morphology After Soft Contact Lens Wear

To evaluate the use of optical coherence tomography (OCT) for assessing the effect of different soft contact lenses on corneoscleral morphology. Ten subjects had anterior segment OCT B-scans taken in the morning and again after 6 h of soft contact lens wear. For each subject, three different contact lenses were used in the right eye on non-consecutive days, including a hydrogel sphere, a silicone hydrogel sphere, and a silicone hydrogel toric. After image registration and layer segmentation, analyses were performed of the first hyper-reflective layer (HRL), the epithelial basement membrane (EBL), and the epithelial thickness (HRL to EBL). A root mean square difference (RMSD) of the layer profiles and the thickness change between the morning and afternoon measurements were used to assess the effect of the contact lens on the corneoscleral morphology. The soft contact lenses had a statistically significant effect on the morphology of the anterior segment layers (p < 0.001). The average amounts of change for the three lenses (average RMSD values) for the corneal region were lower (3.93 ± 1.95 μm for the HRL and 4.02 ± 2.14 μm for the EBL) than those measured in the limbal/scleral region (11.24 ± 6.21 μm for the HRL and 12.61 ± 6.42 μm for the EBL). Similarly, averaged across the three lenses, the RMSD in epithelial thickness was lower in the cornea (2.84 ± 0.84 μm) than the limbal/scleral (5.47 ± 1.71 μm) region. Post hoc analysis showed that ocular surface changes were significantly smaller with the silicone hydrogel sphere lens than both the silicone hydrogel toric (p < 0.005) and hydrogel sphere (p < 0.02) for the combined HRL and EBL data. In this preliminary study, we have shown that soft contact lenses can produce small but significant changes in the morphology of the limbal/scleral region and that OCT technology is useful in assessing these changes. The clinical significance of these changes is yet to be determined.

Effect of yarn extension on migration parameters of fibres in yarns

The present paper deals with a detailed study on the effect of progressive yarn extension on fibre migration. An image processing-based system to characterise and visualise the configuration of fibres in yarn in extended mode has been adopted. A detailed study has been reported on the changes in migration parameters, like mean fibre position (MFP), mean migration intensity (MMI) and root mean square deviation (RMSD), during axial extension of ring-spun yarn. It has been observed that the fibre migration parameters, like MFP, MMI and RSMD, are significantly affected by extension of ring-spun yarn and the trends are different for different levels of extension. It has been observed that the mean fibre position (MFP) increases slightly up to 4% of yarn extension and then decreases up to 8% extension but with a further increase of yarn extension up to 12%, the value of MFP slightly increases again. It has also been reported that with the increase of yarn extension the average RMSD and MMI.

Water requirements and single and dual crop coefficients of sugarcane grown in a tropical region, Brazil

A field experiment was conducted throughout 2009/2010 in a sugarcane field of a commercial distillery located on the coastal area of Paraiba state, Brazil. The objectives were to determine sugarcane water requirements and to test the single and dual crop coefficients by comparing the calculated values of ET with measured ones. Crop evapotranspiration was determined by field water balance, reference evapotranspiration (ETo) by the Penman-Monteith approach, while single and dual crop coefficients were computed through the standard FAO-56 methodology. The experimental area was cultivated with irrigation applied weekly by a centre pivot system in addition to rainfall and the irrigation scheduling was based on 100% ETo. Three statistical tests, mean bias difference (MBD), normalized root mean square difference (NRMSD) and regression analysis, were used to evaluate the performance of single and dual crop coefficients. Results showed that there was a notable symmetry between ET measured and ET calculated by Kc dual. The ET values, calculated from Kc single, underestimated those obtained from soil water balance measurements by 36%.

Measurement of Six Degrees of Freedom Head Kinematics in Impact Conditions Employing Six Accelerometers and Three Angular Rate Sensors (6aω Configuration)

The ability to measure six degrees of freedom (6 DOF) head kinematics in motor vehicle crash conditions is important for assessing head-neck loads as well as brain injuries. A method for obtaining accurate 6 DOF head kinematics in short duration impact conditions is proposed and validated in this study. The proposed methodology utilizes six accelerometers and three angular rate sensors (6aω configuration) such that an algebraic equation is used to determine angular acceleration with respect to the body-fixed coordinate system, and angular velocity is measured directly rather than numerically integrating the angular acceleration. Head impact tests to validate the method were conducted using the internal nine accelerometer head of the Hybrid III dummy and the proposed 6aω scheme in both low (2.3 m/s) and high (4.0 m/s) speed impact conditions. The 6aω method was compared with a nine accelerometer array sensor package (NAP) as well as a configuration of three accelerometers and three angular rate sensors (3aω), both of which have been commonly used to measure 6 DOF kinematics of the head for assessment of brain and neck injuries. The ability of each of the three methods (6aω, 3aω, and NAP) to accurately measure 6 DOF head kinematics was quantified by calculating the normalized root mean squared deviation (NRMSD), which provides an average percent error over time. Results from the head impact tests indicate that the proposed 6aω scheme is capable of producing angular accelerations and linear accelerations transformed to a remote location that are comparable to that determined from the NAP scheme in both low and high speed impact conditions. The 3aω scheme was found to be unable to provide accurate angular accelerations or linear accelerations transformed to a remote location in the high speed head impact condition due to the required numerical differentiation. Both the 6aω and 3aω schemes were capable of measuring accurate angular displacement while the NAP instrumentation was unable to produce accurate angular displacement due to double numerical integration. The proposed 6aω scheme appears to be capable of measuring accurate 6 DOF kinematics of the head in any severity of impact conditions.

Benzene−Pyridine Interactions Predicted by the Effective Fragment Potential Method

The accurate representation of nitrogen-containing heterocycles is essential for modeling biological systems. In this study, the general effective fragment potential (EFP2) method is used to model dimers of benzene and pyridine, complexes for which high-level theoretical data -including large basis spin-component-scaled second-order perturbation theory (SCS-MP2), symmetry-adapted perturbation theory (SAPT), and coupled cluster with singles, doubles, and perturbative triples (CCSD(T))-are available. An extensive comparison of potential energy curves and components of the interaction energy is presented for sandwich, T-shaped, parallel displaced, and hydrogen-bonded structures of these dimers. EFP2 and CCSD(T) potential energy curves for the sandwich, T-shaped, and hydrogen-bonded dimers have an average root-mean-square deviation (RMSD) of 0.49 kcal/mol; EFP2 and SCS-MP2 curves for the parallel displaced dimers have an average RMSD of 0.52 kcal/mol. Additionally, results are presented from an EFP2 Monte Carlo/simulated annealing (MC/SA) computation to sample the potential energy surface of the benzene-pyridine and pyridine dimers.

Calculations of electron inelastic mean free paths. IX. Data for 41 elemental solids over the 50 eV to 30 keV range

AbstractWe have calculated inelastic mean free paths (IMFPs) for 41 elemental solids (Li, Be, graphite, diamond, glassy C, Na, Mg, Al, Si, K, Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Ge, Y, Nb, Mo, Ru, Rh, Pd, Ag, In, Sn, Cs, Gd, Tb, Dy, Hf, Ta, W, Re, Os, Ir, Pt, Au and Bi) for electron energies from 50 eV to 30 keV. The IMFPs were calculated from experimental optical data using the full Penn algorithm for energies up to 300 eV and the simpler single‐pole approximation for higher energies. The calculated IMFPs could be fitted to a modified form of the Bethe equation for inelastic scattering of electrons in matter for energies from 50 eV to 30 keV. The average root‐mean‐square (RMS) deviation in these fits was 0.48%. The new IMFPs were also compared with IMFPs from the predictive TPP‐2M equation; in these comparisons, the average RMS deviation was 12.3% for energies between 50 eV and 30 keV. This RMS deviation is almost the same as that found previously in a similar comparison for the 50 eV–2 keV range. Relatively large RMS deviations were found for diamond, graphite and cesium. If these three elements were excluded in the comparison, the average RMS deviation was 9.2% between 50 eV and 30 keV. We found satisfactory agreement of our calculated IMFPs with IMFPs from recent calculations and from elastic‐peak electron‐spectroscopy experiments. Copyright © 2010 John Wiley &amp; Sons, Ltd.

Performance of Extended Shuttleworth-Wallace Model for Estimating and Partitioning of Evapotranspiration in a Partial Residue-Covered Subsurface Drip-Irrigated Soybean Field

Estimation of actual evapotranspiration (ET), especially its partitioning into plant transpiration (T) and soil evaporation (E), in agricultural fields is important for effective soil water management and conservation and for understanding the interactions between ET, T, and E with the management practices. Direct field measurements of ET, T, and E rates are difficult and costly; hence, mathematical models are used for estimating them. The objective of this study was to evaluate the practical applicability of the Shuttleworth-Wallace (S-W) model to estimate and partition ET in a subsurface drip-irrigated soybean (Glycine max L. Merr.) field with partial residue cover. While its performance has been studied for various surfaces, the performance evaluation of the S-W model for such surface has not been carried out. An integrated approach of calculating bulk stomatal resistance (r s c ) as a function of soil water content (θ i ) was incorporated into the model to allow simulation of T over a range of θ i , and a residue decomposition function was introduced to account for surface residue decay over time to more accurately account for the actual residue cover in field conditions. The model performance was evaluated for different plant growth stages during the 2007 and 2008 growing seasons at the University of Nebraska-Lincoln, South Central Agricultural Laboratory near Clay Center, Nebraska. The sum of estimated T and E was compared to the Bowen Ratio Energy Balance System (BREBS)-measured actual ET on a daily time-step. The model was able to capture the trends and magnitudes of measured ET, but its performance differed for various plant physiological growth stages. The root mean square difference (RMSD) values between the model-estimated and measured ET values for the growing season (day after emergence until physiological maturity) were 1.26 and 1.03 mm d -1 for 2007 and 2008, respectively. Best performance was observed during the mid-season during full canopy cover with a two-year average r 2 of 0.87, average RMSD of 0.94 mm d -1 , and average mean biased error (MBE) of 0.30 mm d -1 . Estimates for both initial and late season growth stages where E was dominant had the least agreement with BREBS measurements. The proportion of T and E in the estimated ET varied with growth stage. The S-W-estimated seasonal total ET and BREBS measurements were equal in 2007 (S-W model ET = 496 mm and BREBS ET = 498 mm), and in 2008 the model underestimated by only 8.2% (S-W model ET = 452 mm and BREBS ET = 489 mm). While, in general, the model was successful in tracking the trends and magnitude of the BREBS-measured ET, further re-parameterization of the T module of the model can improve its accuracy to estimate ET, especially T, during the initial and late season (before full canopy cover and after physiological maturity) for a subsurface drip-irrigated soybean canopy. Other enhancements needed in the model for improved estimation of the E component include accurate determination of soil surface resistance coefficients and accounting for direct evaporation of intercepted rainfall on the canopy.

Bridging the gap between single-template and fragment based protein structure modeling using Spanner

Background: As the coverage of experimentally determined protein structures increases, fragment-based structural modeling approaches are expected to play an ever more important role in structural modeling. Here we introduce a structural modeling method by which an initial structural template can be extended by the addition of structural fragments to more closely match an aligned query sequence. A database of pro-tein fragments indexed by their internal coordinates was created and a novel methodology for their retrieval was implemented. After fragment selection and assembly, sidechains are replaced and the all-atom model is refined by restrained energy minimization. We implemented the proposed method in the program Span-ner and benchmarked it using a previously published set of 367 immunoglobulin (Ig) loops, 206 historical query-template pairs and alignments from the Critical Assessment of protein Structure Prediction (CASP) experiment, and 217 structural alignments between remotely homologous query-template pairs. The con-straint-based modeling software MODELLER and previously reported results for RosettaAntibody, were used as references. Results: The error in the modeled structures was assessed by root-mean square deviation (RMSD) from the native structure, as a function of the query-template sequence identity. For the Ig benchmark set, for which a single fragment was used to model each loop, the average RMSD for Spanner (3 +/- 1.5 A) was found to lie midway between that of MODELLER (4 +/- 2 A) and RosettaAntibody (2 +/- 1 A). For the CASP and structural alignment benchmarks, for which gaps represent a small fraction of the modeled residues, the difference between Spanner and MODELLER were much smaller then the standard deviations of either program. The Spanner web server and source code are available at http://sysimm.ifrec.osaka-u.ac.jp/Spanner/. Conclusions: For typical homology modeling, Spanner is at least as good, on average as the template-free constraint-driven approach used by MODELLER. The Ig model results suggest that when gap regions represent a significant fraction of the alignment, Spanner’s efficient use of fragment libraries, along with local sequence and secondary structural information, significantly improve model accuracy without a dra-matic increase in computational cost.

TASSER_WT: A Protein Structure Prediction Algorithm with Accurate Predicted Contact Restraints for Difficult Protein Targets

To improve the prediction accuracy in the regime where template alignment quality is poor, an updated version of TASSER_2.0, namely TASSER_WT, was developed. TASSER_WT incorporates more accurate contact restraints from a new method, COMBCON. COMBCON uses confidence-weighted contacts from PROSPECTOR_3.5, the latest version, PROSPECTOR_4, and a new local structural fragment-based threading algorithm, STITCH, implemented in two variants depending on expected fragment prediction accuracy. TASSER_WT is tested on 622 Hard proteins, the most difficult targets (incorrect alignments and/or templates and incorrect side-chain contact restraints) in a comprehensive benchmark of 2591 nonhomologous, single domain proteins ≤200 residues that cover the PDB at 35% pairwise sequence identity. For 454 of 622 Hard targets, COMBCON provides contact restraints with higher accuracy and number of contacts per residue. As contact coverage with confidence weight ≥3 ( F wt ≥3 cov ) increases, the more improved are TASSER_WT models. When F wt ≥3 cov > 1.0 and > 0.4, the average root mean-square deviation of TASSER_WT (TASSER_2.0) models is 4.11 Å (6.72 Å) and 5.03 Å (6.40 Å), respectively. Regarding a structure prediction as successful when a model has a TM-score to the native structure ≥0.4, when F wt ≥3 cov > 1.0 and > 0.4, the success rate of TASSER_WT (TASSER_2.0) is 98.8% (76.2%) and 93.7% (81.1%), respectively.

A computational tool for the efficient analysis of dose‐volume histograms for radiation therapy treatment plans

A Histogram Analysis in Radiation Therapy (HART) program was primarily developed to increase the efficiency and accuracy of dose–volume histogram (DVH) analysis of large quantities of patient data in radiation therapy research. The program was written in MATLAB to analyze patient plans exported from the treatment planning system (Pinnacle3) in the American Association of Physicists in Medicine/Radiation Therapy Oncology Group (AAPM/RTOG) format. HART‐computed DVH data was validated against manually extracted data from the planning system for five head and neck cancer patients treated with the intensity‐modulated radiation therapy (IMRT) technique. HART calculated over 4000 parameters from the differential DVH (dDVH) curves for each patient in approximately 10–15 minutes. Manual extraction of this amount of data required 5 to 6 hours. The normalized root mean square deviation (NRMSD) for the HART–extracted DVH outcomes was less than 1%, or within 0.5% distance‐to‐agreement (DTA). This tool is supported with various user‐friendly options and graphical displays. Additional features include optimal polynomial modeling of DVH curves for organs, treatment plan indices (TPI) evaluation, plan‐specific outcome analysis (POA), and spatial DVH (zDVH) and dose surface histogram (DSH) analyses, respectively. HART is freely available to the radiation oncology community.PACS numbers: 87.53.‐j; 87.53.Tf; 87.53.Xd.

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180 000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 Å, for loops up to six residues or <3 Å for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/

Comparison of algorithms for incoming atmospheric long‐wave radiation

While numerous algorithms exist for predicting incident atmospheric long‐wave radiation under clear (Lclr) and cloudy skies, few comparisons have been published to assess the accuracy of the different algorithms. Virtually no comparisons have been made for both clear and cloudy skies across multiple sites. This study evaluates the accuracy of 13 algorithms for predicting incident long‐wave radiation under clear skies, ten cloud correction algorithms, and four algorithms for all‐sky conditions using data from 21 sites across North America and China. Data from five research sites were combined with publicly available data from nine sites in the AmeriFlux network for initial evaluation and optimization of cloud cover estimates; seven additional AmeriFlux sites were used as an independent test of the algorithms. Clear‐sky algorithms that excelled in predicting Lclr were the Dilley, Prata, and Ångström algorithms. Root mean square deviation (RMSD) between predicted and measured 30‐minute or hourly Lclr averaged approximately 23 W m−2 for these three algorithms across all sites, while RMSD of daily estimates was as low as 14 W m−2. Cloud‐correction algorithms of Kimball, Unsworth, and Crawford described the data best when combined with the Dilley clear‐sky algorithm. Average RMSD across all sites for these three cloud corrections was approximately 24 to 25 W m−2 for 30‐minute or hourly estimates and approximately 15 to 16 W m−2 for daily estimates. The Kimball and Unsworth cloud corrections require an estimate of cloud cover, while the Crawford algorithm corrects for cloud cover directly from measured solar radiation. Optimum limits in the clearness index, defined as the ratio of observed solar radiation to theoretical terrestrial solar radiation, for complete cloud cover and clear skies were suggested for the Kimball and Unsworth algorithms. Application of the optimized algorithms to seven independent sites yielded similar results. On the basis of the results, the recommended algorithms can be applied with reasonable accuracy for a wide range of climates, elevations, and latitudes.

Solvent Exposure- and Distance-Dependent Dielectric Function for Ligand-Protein Interactions

Physics-based force fields for high throughput ligand docking usually determine electrostatic energy with distance-dependent dielectric (DDD) functions, which do not fully account for the dielectric permittivity variance between ∼ 2 in the protein core and ∼ 80 at the protein surface. We propose here a new dielectric function that depends on the distance between a pair of interacting atoms and the degree of their exposure to the aqueous environment. This solvent exposure- and distance-depend dielectric (SEDDD) function accounts for both electrostatic and dehydration energy components. Using a training set of ten x-ray structures, we first optimized the global-minimization protocol in the ZMM program with the AMBER force field, implicit solvation, and the DDD function e = 2r. A search was considered a success if the root mean square deviation (RMSD) of the ligand's atoms in the apparent global minimum from the x-ray structure was less than 2 A. For each complex, the apparent global minimum was found by sampling hundreds of thousands of the rigid-ligand binding poses and refining low-energy poses by Monte Carlo-minimizing energy with flexible ligand and flexible protein. For an examining set of 60 structures, the global-minimization protocol with implicit solvation and various DDD functions (e = r, e = 2r, and e =4r) yielded success rates of 66.7%, 73.3% and 75.0% respectively. In most outliers, the ligand-binding sites were located at the protein surface. Using a second training set of 16 ligand-protein complexes, we parameterized the SEDDD function to minimize the average RMSD between the apparent global minima and x-ray structures. Application of the parametrized SEDDD function to the examining set yielded a success rate of 91.7%, a substantial improvement versus the best-performing DDD function with implicit solvation.

Generalized Pattern Search Algorithm for Peptide Structure Prediction

Finding the near-native structure of a protein is one of the most important open problems in structural biology and biological physics. The problem becomes dramatically more difficult when a given protein has no regular secondary structure or it does not show a fold similar to structures already known. This situation occurs frequently when we need to predict the tertiary structure of small molecules, called peptides. In this research work, we propose a new ab initio algorithm, the generalized pattern search algorithm, based on the well-known class of Search-and-Poll algorithms. We performed an extensive set of simulations over a well-known set of 44 peptides to investigate the robustness and reliability of the proposed algorithm, and we compared the peptide conformation with a state-of-the-art algorithm for peptide structure prediction known as PEPstr. In particular, we tested the algorithm on the instances proposed by the originators of PEPstr, to validate the proposed algorithm; the experimental results confirm that the generalized pattern search algorithm outperforms PEPstr by 21.17% in terms of average root mean-square deviation, RMSD C α .

Benchmarking of TASSER_2.0: An Improved Protein Structure Prediction Algorithm with More Accurate Predicted Contact Restraints

To improve tertiary structure predictions of more difficult targets, the next generation of TASSER, TASSER_2.0, has been developed. TASSER_2.0 incorporates more accurate side-chain contact restraint predictions from a new approach, the composite-sequence method, based on consensus restraints generated by an improved threading algorithm, PROSPECTOR_3.5, which uses computationally evolved and wild-type template sequences as input. TASSER_2.0 was tested on a large-scale, benchmark set of 2591 nonhomologous, single domain proteins ≤200 residues that cover the Protein Data Bank at 35% pairwise sequence identity. Compared with the average fraction of accurately predicted side-chain contacts of 0.37 using PROSPECTOR_3.5 with wild-type template sequences, the average accuracy of the composite-sequence method increases to 0.60. The resulting TASSER_2.0 models are closer to their native structures, with an average root mean-square deviation of 4.99 Å compared to the 5.31 Å result of TASSER. Defining a successful prediction as a model with a root mean-square deviation to native <6.5 Å, the success rate of TASSER_2.0 (TASSER) for Medium targets (targets with good templates/poor alignments) is 74.3% (64.7%) and 40.8% (35.5%) for the Hard targets (incorrect templates/alignments). For Easy targets (good templates/alignments), the success rate slightly increases from 86.3% to 88.4%.