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检索条件"任意字段=第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学"

共 191 条记录，以下是11-20 订阅

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DNA conformations and Inter-Base-Pairs hydrogen bonds

DNA conformations and Inter-Base-Pairs hydrogen bonds

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xuqing Li Ping Fan Department of Biomedical Engineering Kunming University of Science and Technology

By studying DNA fine structure and physical properties at dinucleotide step level,we have proposed and published that,besides W-C pairing Hydrogen bonds,DNA duplex should contain regular Inter-Base-Pair hydrogen bonds(IBP H-Bonds),which result from the recent studying about non-planarity of amino groups in DNA *** analyzing the IBP H-Bonds containing DAN helical fragments of defined-sequence oligonucleotides,we found that there are correlations between the DNA helical conformations and IBP *** results imply that the IBP H-Bonds is very important factor in determining DNA helical conformations.

关键词： DNA helical conformations Inter-base-pairs hydrogen bonds Sequence-dependence

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Prediction of human protein ubiquitylation sites based on the sequence signatures

Prediction of human protein ubiquitylation sites based on th...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Bing He Xiaofcng Song Department of Biomedical Engineering Nanjing University of Aeronautics and Astronautics

Ubiquitylation is one of the most popular post-translational modifications(PTM), which plays important roles in directing the protein ***,identification of ubiquitylation sites is essential for comprehensively understanding the regulation of ubiquitylation process and the molecular mechanisms of protein selective *** this study,we constructed new computational models with a statistical learning method,support vector machine(SVM),to predict human ubiquitylation sites from sequence segments. The results indicated that provide further evidence that some sequence features such as physicochemical properties of amino acids can be used to identify the protein ubiquitylation *** new computational method provided an alternative tool for rapidly identifying the ubiquitylation sites of human protein.

关键词： ubiquitylation site support vector machine sequence signatures

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Application of the information dynamic function in prediction of protein folding rate

Application of the information dynamic function in predictio...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Jianzhao Gao Yajun Sheng Gang Hu Kui Wang Shiyi Shen Jishou Ruan the school of mathematical sciences and LPMC Nankai University

Background:Protein folding rates vary by several orders of magnitude and they depend on the topology of the fold and the size and composition of the sequence. Methods:We proposed an new method to predict the folding rate which is based on the information dynamic function. Results:The predictor includes three linear regressions for proteins with two-state, multi-state,and unknown(mixed-state) folding *** method achieves the correlation 0.9 for two-state,0.86 for multistate and 0.85 for *** with other methods, our method achieves higher correlation. Conclusions:Our method can be used to predict the folding *** provides a new way to understand the folding rate.

关键词： information dynamic function protein folding rate linear regression

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HOPF Bifurcation in Regulatory Biological Networks

HOPF Bifurcation in Regulatory Biological Networks

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Liping Zhang Yuying Wang Faculty of Science Nanjing University of Aeronautics and Astronautics Faculty of Science xi'an Jiaotong University

Recent experiment have shown that the oscillatory behavors for the activities p53 and Mdm2 proteins in respect to DNA damage,we propose a new nonlinear dynamics with three delays to describe the p53-mdm2 *** choosing the delay as a bifurcation parameter,The stability and the existence of bifurcation are researched in this *** particular,the formulae determining the direction of the bifurcations and the stability of the bifurcating periodic solutions are derived by using the normal form theory and center manifold *** proposed mathematical method have the significance in the problems,as well as the time delays have the characteristic biological ***,numerical simulations supporting the theoretical analysis are also given.

关键词： p53-Mdm2 Interaction Negative Feedback Loop Hopf bifurcation,delay

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incRNA:Characterizing novel ncRNAs by integrating high-throughput data and structure predictions

incRNA:Characterizing novel ncRNAs by integrating high-throu...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：鲁志 MOE Key Lab of Bioinformatics School of Life ScienceTsinghua University

I will present an integrative,machine-learning method,incRNA,for whole-genome identification of non-coding RNAs(ncRNAs).It combines a large amount of expression data,epigenetics data,RNA secondary-structure stability,and evolutionary conservation at the protein and nucleic-acid *** this model,we were able to separate known ncRNAs from coding sequences and other genomic elements with high accuracy(>93% AUC on an independent validation set),and find thousands of novel ncRNA candidates in *** and Arabidopsis. In addition,we characterized the novel ncRNA candidates and found that they have distinct expression patterns across developmental stages,tend to use novel RNA structural families,and are targeted by specific transcription ***,our study identifies many new potential ncRNAs in different systems.

关键词： incRNA:Characterizing novel ncRNAs by integrating high-throughput data and structure predictions

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Understanding the Molecular Mechanisms of Aging:Modern Approaches to an Ancient Problem

Understanding the Molecular Mechanisms of Aging:Modern Appro...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：李好 UCSF

Aging is a universal *** species age,including *** aging seems inevitable,dreams for immortality started early in human *** many attempts had been made to cure or slow down aging,and they all *** the last few decades,application of molecular genetics to the study of aging has led to the surprising discovery that the lifespan of a species is plastic and can be manipulated by simple genetic or dietary changes,raising the hope that we may be able to significantly extend the human lifespan and at the same time prevent or cure aging related *** this talk,I will first give an overview of the modern field of molecular genetics of aging.I will then discuss how systems biology approaches can be used to define the molecular mechanisms of *** particular,I will describe a novel microfluidic system that we have developed to study aging in single yeast *** system allows,for the first time,the direct visualization of various cellular and molecular events accompanying aging in single cells throughout their lifespan, leading to new insight into the mechanisms of cellular aging and death.

关键词： Understanding the Molecular Mechanisms of Aging:Modern Approaches to an Ancient Problem

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Structural Bioinformatics and Chinese Traditional Medicine Database For Drug Design

Structural Bioinformatics and Chinese Traditional Medicine D...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：魏冬青 Ruo-Xu Gu State Key Lab.Of Microbial Metabolism and College of Life Science and Biotechnology Shanghai Jiaotong University

Structural bioinformatics tools and databases have been developed and applied to study diversified biological *** modeling tools were developed to generate 3D structure from sequences of novel *** allows us pursue structure based drug design. Applications were made to drug design for SARS,H5N1 and HIV.A octapeptide AVLQSGFR designed by us was synthesized and its antiviral potential against SARS coronavirus(BJ-01) was assessed,which demonstrates that AVLQSGFR is the most active in inhibiting replication of the SARS coronavirus compared with other compounds reported so far(EC50 is 2.7×10- 2mg/L,and its selectivity index is more than 3704),while no detectable toxicity on Vero cells under the condition of experimental concentration is observed.

关键词： Structural Bioinformatics and Chinese Traditional Medicine Database For Drug Design

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Bridging modern and traditional Chinese medicines by knowledge-mining

Bridging modern and traditional Chinese medicines by knowled...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xiaoqin Yang Xinyi Hang Sheng Chen Xuezhong Zhou Ling Yin Shuang Liang Telemedicine Center Institute of Medical InformaticsGeneral Hospital of Chinese PLA

Background:Unlike Western medicine,Traditional Chinese Medicine(TCM),which is based on the doctrine and empirical practices of systems science,uses simple yet meaningful symptoms or their combinations to describe ***,the theory behind each symptom is often obscure for the lack of scientific basis and molecule evidence as compared to modern medicine. Methods:A significant effort has been made to link TCM symptoms and standard disease terms by common genes using text mining. Results:The current release carefully selected 4,989 gene-symptom relationships, covering 80 TCM ***,TCMeSH can also be used as a discovery tool by generating novel inferences. Conclusions:Some inherently useful but hidden relations among genes,diseases,TCM symptoms can be inferred to form testable hypotheses.

关键词： Disease Symptom TCM

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An algorithm to measuring protein curvature based on the protein SES atoms

An algorithm to measuring protein curvature based on the pro...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Yujiao Yan Xiaofeng Song Department of Biomedical Engineering Nanjing University of Aeronautics and Astronautics

Molecular surface plays an important role in analyzing protein molecular structure and *** of protein-protein interaction sites using surface curvature and shape index is an important method to study the protein function based on molecular structure. Therefore,accurate calculations of molecular curvature are *** paper presents an algorithm to measuring protein surface curvature based on the protein molecular surface *** calculates the normal vectors of surface atoms through the rational modeling from the SES,and then obtains the curvature and shape index of the molecular surface *** these parameters,we can identify the convex surfaces and concave *** results can be directly displayed on the SES model and colored according to shape index values,we can intuitively observe the protein-protein interaction sites and the shape of ligands binding to the *** provides the key clues to predicting the protein docking and new drugs research.

关键词： protein molecular surface curvature shape index protein-protein interaction docking

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Toward Improving Protein-Ligand Binding Energy Computation

Toward Improving Protein-Ligand Binding Energy Computation

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Shijun Zhong School of Life Science and Technology Dalian University of Technology

Background:Protein-ligand interaction plays a key role in controlling biological *** the computation of protein-ligand binding energy is a crucial step in computer aided drug *** to the huge amount of computational tasks in virtual screening and the complexity of protein-ligand systems,scoring functions with a lot of approximations are used other than accurate free energy *** lets to low hit-to-lead rate. Methods:Quantum chemistry computations with new Gaussian basis sets and molecular dynamics simulations with the force field of drug molecules were used to improve the accuracy of protein-ligand binding energy *** approaches were also used with respect to the ligand binding selectivity and molecular properties of drug-like compounds. Results:The accuracy of protein-ligand binding energy computation can be improved by introducing quantum chemistry correction and proper scaling. Conclusions:Higher accuracy of protein-ligand binding energy computation will be used to improve the efficiency of computer-aided drug design.

关键词： protein-ligand interaction binding energy computational accuracy drug design

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