New statistical potentials for improved protein structure prediction

This dissertation presents a new scheme to derive four-body contact potentials as a way to consider protein interactions in a more cooperative model. These new four-body contact potentials, noted as SET1 four-body contact potentials (sequential information included), show important gains in threading. SET2 four-body contact potentials (non-sequential information included) have also been developed to supplement SET1 by including spatial information. In addition to SET1 and SET2, we also include the short-range conformational energies introduced by us previously in threading. The combination of these different potentials shows significant improvement in threading tests of some decoy sets. Protein packing is an important aspect of computational structural biology. Icosahedron is chosen as an ideal model to fit the protein packing clusters from a set of protein structures. A theoretical description of packing patterns and packing regularities of icosahedron has been proposed. We find that the order parameter (orientation function) measuring the angular overlap of directions in coordination clusters with directions of the icosahedron is 0.91, which is a significant improvement in comparison with the value 0.82 for the order parameter with the face-centered cubic (fcc) lattice. Close packing tendencies and patterns of residue packing in proteins is considered in detail and a theoretical description of these packing regularities is proposed. Protein motion is another important field. The elastic network interpolation (ENI) model has been used to generate conformational transition intermediates of adenylate kinase (AK) based only C alpha atoms. We construct the atomistic intermediates by grafting all the other atoms except C alpha from the open form AK and then performing CHARMM energy minimization to remove steric conflicts and optimize the intermediate structures. We compare the free energy profiles for all intermediates from both CHARMM force field and statistical energy functions. And we find CHARMM total free energies can successfully captures the two energy minima representing the open form AK and the closed form AK, however the free energies from statistical energy functions can detect the energy minimum representing the semi-closed intermediate with LID domain closed and NMP domain open and the local energy minimum representing the closed form AK

Third Party Logistics in E-Commerce Environment in China

With the rapid development of IT technology, e-commerce plays an increasingly important role nowadays. Since logistics is vital for e-commerce, it becomes the key factor for any corporate in order to survive in the fierce competition. However, logistics industry is not considered as important as other industries in China and few attempts has have been made in this field. The purpose of this paper was to present the current situation of third party logistics under e-commerce and their close relationship.Another goal was to arouse more attention to third party logistics. The objective was to analyze the exsisting problems in the logistics process and put forward solutions accordingly. This thesis is made up of two parts, the theoretical part and the empirical part. The first part gives an overview of e-commerce and third party logistics. In the second part, Xunjie company was selected as a case company to make theory serve reality. The theory which is discussed in the first part is applied to solve the issues in Xunjie company. The research of the thesis is based on a qualitative interview with a manager of Xunjie. Based on the interview and the analysis of the current situation of 3PL, the development of 3PL shoes a positive growing trend although there are some issues and challenges that cannot be ignored. This paper provides readers with an overview of third party logistics, which deserves more attention

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

<p>Abstract</p> <p>Background</p> <p>Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.</p> <p>Results</p> <p>Our new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.</p> <p>Conclusions</p> <p>Our Potentials 'R'Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.</p

Characterizing Immunoglobulin Repertoire from Whole Blood by a Personal Genome Sequencer

In human immune system, V(D)J recombination produces an enormously large repertoire of immunoglobulins (Ig) so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(D)J recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(D)J recombination within a day by personal genome sequencers

The spatial distribution and temporal variation of desert riparian forests and their influencing factors in the downstream Heihe River basin, China

Desert riparian forests are the main restored vegetation community in Heihe River basin. They provide critical habitats and a variety of ecosystem services in this arid environment. Since desert riparian forests are also sensitive to disturbance, examining the spatial distribution and temporal variation of these forests and their influencing factors is important to determine the limiting factors of vegetation recovery after long-term restoration. In this study, field experiment and remote sensing data were used to determine the spatial distribution and temporal variation of desert riparian forests and their relationship with the environmental factors. We classified five types of vegetation communities at different distances from the river channel. Community coverage and diversity formed a bimodal pattern, peaking at the distances of 1000 and 3000 m from the river channel. In general, the temporal normalized difference vegetation index (NDVI) trend from 2000 to 2014 was positive at different distances from the river channel, except for the region closest to the river bank (i.e. within 500 m from the river channel), which had been undergoing degradation since 2011. The spatial distribution of desert riparian forests was mainly influenced by the spatial heterogeneity of soil properties (e.g. soil moisture, bulk density and soil particle composition). Meanwhile, while the temporal variation of vegetation was affected by both the spatial heterogeneity of soil properties (e.g. soil moisture and soil particle composition) and to a lesser extent, the temporal variation of water availability (e.g. annual average and variability of groundwater, soil moisture and runoff). Since surface (0–30 cm) and deep (100–200 cm) soil moisture, bulk density and the annual average of soil moisture at 100 cm obtained from the remote sensing data were regarded as major determining factors of community distribution and temporal variation, conservation measures that protect the soil structure and prevent soil moisture depletion (e.g. artificial soil cover and water conveyance channels) were suggested to better protect desert riparian forests under climate change and intensive human disturbance

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

We propose a novel method of calculation of free energy for coarse grained models of proteins by combining our newly developed multibody potentials with entropies computed from elastic network models of proteins. Multi-body potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Combining four-body non-sequential, four-body sequential and pairwise short range potentials with optimized weights for each term, our coarse-grained potential improved recognition of native structure among misfolded decoys, outperforming all other contact potentials for CASP8 decoy sets and performance comparable to the fully atomic empirical DFIRE potentials. By combing statistical contact potentials with entropies from elastic network models of the same structures we can compute free energy changes and improve coarse-grained modeling of protein structure and dynamics. The consideration of protein flexibility and dynamics should improve protein structure prediction and refinement of computational models. This work is the first to combine coarse-grained multibody potentials with an entropic model that takes into account contributions of the entire structure, investigating native-like decoy selection