A tool for calculating binding-site residues on proteins from PDB structures

<p>Abstract</p> <p>Background</p> <p>In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB) that consists of the protein of interest and its interacting partner(s) and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice.</p> <p>Results</p> <p>In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP <url>http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit</url>. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues.</p> <p>Conclusion</p> <p>The developed tool is very useful for the research on protein binding site analysis and prediction.</p

HMM_RA: An Improved Method for Alpha-Helical Transmembrane Protein Topology Prediction

α-helical transmembrane (TM) proteins play important and diverse functional roles in cells. The ability to predict the topology of these proteins is important for identifying functional sites and inferring function of membrane proteins. This paper presents a Hidden Markov Model (referred to as HMM_RA) that can predict the topology of α-helical transmembrane proteins with improved performance. HMM_RA adopts the same structure as the HMMTOP method, which has five modules: inside loop, inside helix tail, membrane helix, outside helix tail and outside loop. Each module consists of one or multiple states. HMM_RA allows using reduced alphabets to encode protein sequences. Thus, each state of HMM_RA is associated with n emission probabilities, where n is the size of the reduced alphabet set. Direct comparisons using two standard data sets show that HMM_RA consistently outperforms HMMTOP and TMHMM in topology prediction. Specifically, on a high-quality data set of 83 proteins, HMM_RA outperforms HMMTOP by up to 7.6% in topology accuracy and 6.4% in α-helices location accuracy. On the same data set, HMM_RA outperforms TMHMM by up to 6.4% in topology accuracy and 2.9% in location accuracy. Comparison also shows that HMM_RA achieves comparable performance as Phobius, a recently published method

Hyperspectral LiDAR-Based Plant Spectral Profiles Acquisition : Performance Assessment and Results Analysis

In precision agriculture, efficient fertilization is one of the most important pursued goals. Vegetation spectral profiles and the corresponding spectral parameters are usually employed for vegetation growth status indication, i.e., vegetation classification, bio-chemical content mapping, and efficient fertilization guiding. In view of the fact that the spectrometer works by relying on ambient lighting condition, hyperspectral/multi-spectral LiDAR (HSL/MSL) was invented to collect the spectral profiles actively. However, most of the HSL/MSL works with the wavelength specially selected for specific applications. For precision agriculture applications, a more feasible HSL capable of collecting spectral profiles at wide-range spectral wavelength is necessary to extract various spectral parameters. Inspired by this, in this paper, we developed a hyperspectral LiDAR (HSL) with 10 nm spectral resolution covering 500~1000 nm. Different vegetation leaf samples were scanned by the HSL, and it was comprehensively assessed for wide-range wavelength spectral profiles acquirement, spectral parameters extraction, vegetation classification, and the laser incident angle effect. Specifically, three experiments were carried out: (1) spectral profiles results were compared with that from a SVC spectrometer (HR-1024, Spectra Vista Corporation); (2) the extracted spectral parameters from the HSL were assessed, and they were employed as the input features of a support vector machine (SVM) classifier with multiple labels to classify the vegetation; (3) in view of the influence of the laser incident angle on the HSL reflected laser intensities, we analyzed the laser incident angle effect on the spectral parameters values. The experimental results demonstrated the developed HSL was more feasible for acquiring spectral profiles with wide-range wavelength, and spectral parameters and vegetation classification results also indicated its great potentials in precision agriculture application

Analysis and Radiometric Calibration for Backscatter Intensity of Hyperspectral LiDAR Caused by Incident Angle Effect

Hyperspectral LiDAR (HSL) is a new remote sensing detection method with high spatial and spectral information detection ability. In the process of laser scanning, the laser echo intensity is affected by many factors. Therefore, it is necessary to calibrate the backscatter intensity data of HSL. Laser incidence angle is one of the important factors that affect the backscatter intensity of the target. This paper studied the radiometric calibration method of incidence angle effect for HSL. The reflectance of natural surfaces can be simulated as a combination of specular reflection and diffuse reflection. The linear combination of the Lambertian model and Beckmann model provides a comprehensive theory that can be applied to various surface conditions, from glossy to rough surfaces. Therefore, an adaptive threshold radiometric calibration method (Lambertian-Beckmann model) is proposed to solve the problem caused by the incident angle effect. The relationship between backscatter intensity and incident angle of HSL is studied by combining theory with experiments, and the model successfully quantifies the difference between diffuse and specular reflectance coefficients. Compared with the Lambertian model, the proposed model has higher calibration accuracy, and the average improvement rate to the samples in this study was 22.67%. Compared with the results before calibration with the incidence angle of less than 70 degrees, the average improvement rate of the Lambertian-Beckmann model was 62.26%. Moreover, we also found that the green leaves have an obvious specular reflection effect near 650-720 nm, which might be related to the inner microstructure of chlorophyll. The Lambertian-Beckmann model was more helpful to the calibration of leaves in the visible wavelength range. This is a meaningful and a breakthrough exploration for HSL.Peer reviewe

Review on Active and Passive Remote Sensing Techniques for Road Extraction

Digital maps of road networks are a vital part of digital cities and intelligent transportation. In this paper, we provide a comprehensive review on road extraction based on various remote sensing data sources, including high-resolution images, hyperspectral images, synthetic aperture radar images, and light detection and ranging. This review is divided into three parts. Part 1 provides an overview of the existing data acquisition techniques for road extraction, including data acquisition methods, typical sensors, application status, and prospects. Part 2 underlines the main road extraction methods based on four data sources. In this section, road extraction methods based on different data sources are described and analysed in detail. Part 3 presents the combined application of multisource data for road extraction. Evidently, different data acquisition techniques have unique advantages, and the combination of multiple sources can improve the accuracy of road extraction. The main aim of this review is to provide a comprehensive reference for research on existing road extraction technologies.Peer reviewe