Predicting octanol/water partition coefficient using solvation free energy and solvent-accessible surface area

The regression model for octanol/water partition coefficients ( K ow ), is founded with only two molecular descriptors available through quantum chemical calculations: solvation free energy (Δ G S ), and solvent accessible surface area (SASA). For the properties of 47 organic compounds from 17 types, the model gives a correction coefficient (adjusted for degrees of freedom) of 0 959 and a standard error of 0 277 log unit. It is a suitable way to predict the partition properties that are related to solute solvent interactions in the water phase.

Estimating walking access area for rail transit station based on discrete choice model

The discrete choice model is used to estimate the walking access area of rail transit stations while considering the influence of existing competition from other traffic modes. The acceptable walking access area is determined according to the willingness of passengers to walk who prefer rail transit compared with bus and automobile. Empirical studies were conducted using the survey data of six stations from the rail transit in Nanjing, China. The results indicate that the rail transit is more preferable compared with bus and private automobile in this case when excluding the influence of individual and environmental factors. It is found that passengers tend to underestimate their willingness to walk. The acceptable walking access area of every rail transit station is different from each other. Suburban stations generally have a larger walking access area than downtown stations. In addition, a better walking environment and a scarcer surrounding traffic environment can also lead to a larger walking area. The model was confirmed to be effective and reasonable according to the model validation. This study can be of benefit to the passenger transportation demand estimation in the location planning and evaluation of rail transit stations.

Mem Brain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction

Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane proteins.Mem Brain web server is free for academic use and available at www.csbio.sjtu.edu.cn/bioinf/Mem Brain/.

Modeling and Simulation of P-Aloha,CSMA /CA and MACAW Protocols for Underwater Acoustic Channel

Medium access control( MAC) protocol of underwater acoustic communication network is a key technology for underwater acoustic networks( UANs). Most of the MAC protocols for wireless terrestrial communication networks have been designed with negligible propagation delay. If it is deployed directly in an underwater environment,the UANs will perform inefficiently. In this paper,the characteristics of underwater acoustic channel are modeled and simulated by using the OPNET simulation tool,which are the speed of sound, propagation loss, and four sources for ambient noise: the turbulence,shipping,wind driven waves and thermal noise. The performance of pure Aloha( P-Aloha),carrier sense multiple access with collision avoidance( CSMA / CA) and multiple access collision avoidance for wireless local area network( MACAW) protocols in underwater acoustic channel environment are evaluated. The different performance of protocols in underwater environment is compared in the simulation.

Influences of the Hydrophobicity of the Heme-binding Pocket on the Properties and Functions of Cytochrome b_5 Mutants

The mutation sites of the four mutants F35Y, P40V, V45E and V45Y of cytochrome b 5 are located at the edge of the heme binding pocket. The solvent accessible areas of the “pocket interior” of the four mutants and the wild type cytochrome b 5 have been calculated based on their crystal structures at high resolution. The change in the hydrophobicity of the heme binding pocket resulting from the mutation can be quantitatively described using the difference of the solvent accessible area of the “pocket interior” of each mutant from that of the wild type cytochrome b 5. The influences of the hydrophobicity of the heme binding pocket on the protein stability and redox potential are discussed.