检索结果-内蒙古大学图书馆

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

引用

BMC BIOINFORMATICS 2010年第1期11卷 231-231页

作者： Popenda, Mariusz Szachniuk, Marta Blazewicz, Marek Wasik, Szymon Burke, Edmund K. Blazewicz, Jacek Adamiak, Ryszard W. Polish Acad Sci Inst Bioorgan Chem Poznan Poland Poznan Univ Tech Inst Comp Sci Poznan Poland Poznan Supercomp & Networking Ctr Poznan Poland Univ Nottingham Automated Scheduling Optimisat & Planning Grp Sch Comp Sci Nottingham NG7 2RD England

Background: Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description: RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE

关键词： protein data bank Menu Item Conformational Parameter protein data bank file Dinucleotide Step

来源：评论

学校读者我要写书评

暂无评论

Inhibition of the NEMO/IKKβ association complex formation, a novel mechanism associated with the NF-κB activation suppression by Withania somnifera's key metabolite withaferin A

引用

BMC GENOMICS 2010年第4-Sup期11卷 S25-S25页

作者： Grover, Abhinav Shandilya, Ashutosh Punetha, Ankita Bisaria, Virendra S. Sundar, Durai Indian Inst Technol Dept Biochem Engn & Biotechnol New Delhi 110016 India Indian Inst Technol Supercomp Facil Bioinformat & Computat Biol New Delhi 110016 India

Background: Nuclear Factor kappa B (NF-kappa B) is a transcription factor involved in the regulation of cell signaling responses and is a key regulator of cellular processes involved in the immune response, differentiation, cell proliferation, and apoptosis. The constitutive activation of NF-kappa B contributes to multiple cellular outcomes and pathophysiological conditions such as rheumatoid arthritis, asthma, inflammatory bowel disease, AIDS and cancer. Thus there lies a huge therapeutic potential beneath inhibition of NF-kappa B signalling pathway for reducing these chronic ailments. Withania somnifera, a reputed herb in ayurvedic medicine, comprises a large number of steroidal lactones known as withanolides which show plethora of pharmacological activities like anti-inflammatory, antitumor, antibacterial, antioxidant, anticonvulsive, and immunosuppressive. Though a few studies have been reported depicting the effect of WA (withaferin A) on suppression of NF-kappa B activation, the mechanism behind this is still eluding the researchers. The study conducted here is an attempt to explore NF-kappa B signalling pathway modulating capability of Withania somnifera's major constituent WA and to elucidate its possible mode of action using molecular docking and molecular dynamics simulations studies. Results: Formation of active IKK (I kappa B kinase) complex comprising NEMO (NF-kappa B Essential Modulator) and IKK beta subunits is one of the essential steps for NF-kappa B signalling pathway, non-assembly of which can lead to prevention of the above mentioned vulnerable disorders. As observed from our semi-flexible docking analysis, WA forms strong intermolecular interactions with the NEMO chains thus building steric as well as thermodynamic barriers to the incoming IKK beta subunits, which in turn pave way to naive complex formation capability of NEMO with IKK beta. Docking of WA into active NEMO/IKK beta complex using flexible docking in which key residues of the comple

关键词： Molecular Dynamics Simulation protein data bank Docking Simulation Lamarckian Genetic Algorithm protein data bank file

来源：评论

学校读者我要写书评

暂无评论

In silico modeling of the specific inhibitory potential of thiophene-2,3-dihydro-1,5-benzothiazepine against BChE in the formation of β-amyloid plaques associated with Alzheimer's disease

引用

THEORETICAL BIOLOGY AND MEDICAL MODELLING 2010年第6期7卷 22-22页

作者： Ul-Haq, Zaheer Khan, Waqasuddin Kalsoom, Saima Ansari, Farzana L. Univ Karachi Int Ctr Chem & Biol Sci Dr Panjwani Ctr Mol Med & Drug Res Karachi 75270 Pakistan Quaid I Azam Univ Dept Chem Islamabad 45320 Pakistan

Background: Alzheimer's disease, known to be associated with the gradual loss of memory, is characterized by low concentration of acetylcholine in the hippocampus and cortex part of the brain. Inhibition of acetylcholinesterase has successfully been used as a drug target to treat Alzheimer's disease but drug resistance shown by butyrylcholinesterase remains a matter of concern in treating Alzheimer's disease. Apart from the many other reasons for Alzheimer's disease, its association with the genesis of fibrils by beta-amyloid plaques is closely related to the increased activity of butyrylcholinesterase. Although few data are available on the inhibition of butyrylcholinesterase, studies have shown that that butyrylcholinesterase is a genetically validated drug target and its selective inhibition reduces the formation of beta-amyloid plaques. Rationale: We previously reported the inhibition of cholinesterases by 2,3-dihydro-1, 5-benzothiazepines, and considered this class of compounds as promising inhibitors for the cure of Alzheimer's disease. One compound from the same series, when substituted with a hydroxy group at C-3 in ring A and 2-thienyl moiety as ring B, showed greater activity against butyrylcholinesterase than to acetylcholinesterase. To provide insight into the binding mode of this compound (Compound A), molecular docking in combination with molecular dynamics simulation of 5000 ps in an explicit solvent system was carried out for both cholinesterases. Conclusion: Molecular docking studies revealed that the potential of Compound A to inhibit cholinesterases was attributable to the cumulative effects of strong hydrogen bonds, cationic-pi, pi-pi interactions and hydrophobic interactions. A comparison of the docking results of Compound A against both cholinesterases showed that amino acid residues in different sub-sites were engaged to stabilize the docked complex. The relatively high affinity of Compound A for butyrylcholinesterase was due to the additional

关键词： protein data bank Root Mean Square Deviation Catalytic Triad Docking Protocol protein data bank file

来源：评论

学校读者我要写书评

暂无评论

ProDaMa: An open source Python library to generate protein structure datasets

引用

BMC Research Notes 2009年第1期2卷 1-4页

作者： Armano, Giuliano Manconi, Andrea Department of Electrical and Electronic Engineering University of Cagliari 09123 Cagliari P.zza D'Armi Italy

Background. The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. Findings. To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. Conclusion. ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL http://***/prodama. © 2009 Manconi et al.

关键词： protein data bank Local database Filter Operator Specialized dataset protein data bank file

来源：评论

学校读者我要写书评

暂无评论

Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display

引用

BMC BIOINFORMATICS 2009年第1期10卷 103-103页

作者： Pal, Arumay Bahadur, Ranjit Prasad Ray, Partha Sarathi Chakrabarti, Pinak Bose Inst Dept Biochem Kolkata 700054 India Bose Inst Bioinformat Ctr Kolkata 700054 India

Background: Depending on chemical features residues have preferred locations-interior or exterior-in protein structures, which also determine how many other residues are found around them. The close packing of residues is the hallmark of protein interior and protein-protein interaction sites. Results: The average values of accessible surface area (ASA) and partner number (PN, the number of other residues within a distance of 4.5 angstrom from any atom of a given residue) of different residues have been determined and a webserver, ContPlot has been designed to display these values (relative to the average values) along the protein sequence. This would be useful to visually identify residues that are densely packed, or those involved in protein-protein interactions. The skewness observed in the distribution of PNs is indicative of the hydrophobic or hydrophilic nature of the residue. The variation of ASA with PN can be analytically expressed in terms of a cubic equation. These equations (one for each residue) can be used to estimate the ASA of a polypeptide chain using the PNs of the individual residues in the structure. Conclusion: The atom-based PNs (obtained by counting surrounding atoms) are highly correlated to the residue-based PN, indicating that the latter can adequately capture the atomic details of packing. The average values of ASA and PN associated with each residue should be useful in protein structure prediction or fold-recognition algorithm. ContPlot would provide a handy tool to assess the importance of a residue in the protein structure or interaction site.

关键词： protein data bank Hydrophobic Residue Accessible Surface Area Solvent Accessible Surface Area protein data bank file

来源：评论

学校读者我要写书评

暂无评论

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

引用

JOURNAL OF CHEMINFORMATICS 2009年第1期1卷 13-13页

作者： Lippert, Tobias Rarey, Matthias Ctr Bioinformat D-20146 Hamburg Germany

Background: Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results: We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion: Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.

关键词： protein data bank Hydrogen Bond Network Dynamic Programming Approach Interaction Score protein data bank file

来源：评论

学校读者我要写书评

暂无评论

PDA: an automatic and comprehensive analysis program for protein-DNA complex structures

引用

BMC GENOMICS 2009年第Sup1期10卷 S13-S13页

作者： Kim, RyangGuk Guo, Jun-tao Univ N Carolina Coll Comp & Informat Dept Bioinformat & Genom Charlotte NC 28223 USA

Background: Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation. Although over 1400 protein-DNA complex structures have been deposited into protein data bank (PDB), the structural details of protein-DNA interactions are generally not available. In addition, current approaches to comparison of protein-DNA complexes are mainly based on protein sequence similarity while the DNA sequences are not taken into account. With the number of experimentally-determined protein-DNA complex structures increasing, there is a need for an automatic program to analyze the protein-DNA complex structures and to provide comprehensive structural information for the benefit of the whole research community. Results: We developed an automatic and comprehensive protein-DNA complex structure analysis program, PDA (for protein-DNA complex structure analyzer). PDA takes PDB files as inputs and performs structural analysis that includes 1) whole protein-DNA complex structure restoration, especially the reconstruction of double-stranded DNA structures;2) an efficient new approach for DNA base-pair detection;3) systematic annotation of protein-DNA interactions;and 4) extraction of DNA subsequences involved in protein-DNA interactions and identification of protein-DNA binding units. protein-DNA complex structures in current PDB were processed and analyzed with our PDA program and the analysis results were stored in a database. A dataset useful for studying protein-DNA interactions involved in gene regulation was generated using both protein and DNA sequences as well as the contact information of the complexes. WebPDA was developed to provide a web interface for using PDA and for data retrieval. Conclusion: PDA is a computational tool for structural annotations of protein-DNA complexes. It provides a useful resource for investigating protein-DNA interactions. data from the PDA analysis can also facilitat

关键词： protein data bank Matthews Correlation Coefficient protein data bank file protein data bank Entry Stagger Distance

来源：评论

学校读者我要写书评

暂无评论

SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase

引用

BMC BIOINFORMATICS 2008年第1期9卷 1-12页

作者： David, Fabrice P. A. Yip, Yum L. Swiss Inst Bioinformat Swiss Prot Grp CH-1211 Geneva Switzerland Univ Geneva Dept Struct Biol & Bioinformat CH-1211 Geneva Switzerland

Background: Sequences and structures provide valuable complementary information on protein features and functions. However, it is not always straightforward for users to gather information concurrently from the sequence and structure levels. The UniProt knowledgebase (UniProtKB) strives to help users on this undertaking by providing complete cross-references to protein data bank (PDB) as well as coherent feature annotation using available structural information. In this study, SSMap - a new UniProt-PDB residue-residue level mapping - was generated. The primary objective of this mapping is not only to facilitate the two tasks mentioned above, but also to palliate a number of shortcomings of existent mappings. SSMap is the first isoform sequence-specific mapping resource and is up-to-date for UniProtKB annotation tasks. The method employed by SSMap differs from the other mapping resources in that it stresses on the correct reconstruction of the PDB sequence from structures, and on the correct attribution of a UniProtKB entry to each PDB chain by using a series of post-processing steps. Results: SSMap was compared to other existing mapping resources in terms of the correctness of the attribution of PDB chains to UniProtKB entries, and of the quality of the pairwise alignments supporting the residue-residue mapping. It was found that SSMap shared about 80% of the mappings with other mapping sources. New and alternative mappings proposed by SSMap were mostly good as assessed by manual verification of data subsets. As for local pairwise alignments, it was shown that major discrepancies (both in terms of alignment lengths and boundaries), when present, were often due to differences in methodologies used for the mappings. Conclusion: SSMap provides an independent, good quality UniProt-PDB mapping. The systematic comparison conducted in this study allows the further identification of general problems in UniProt-PDB mappings so that both the coverage and the quality of the ma

关键词： protein data bank Alternative Mapping Mapping Resource protein data bank file protein data bank Entry

来源：评论

学校读者我要写书评

暂无评论

Proteopedia -: a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules

引用

GENOME BIOLOGY 2008年第8期9卷 R121-R121页

作者： Hodis, Eran Prilusky, Jaime Martz, Eric Silman, Israel Moult, John Sussman, Joel L. Weizmann Inst Sci Israel Struct Prote Ctr IL-76100 Rehovot Israel Weizmann Inst Sci Biol Serv Unit IL-76100 Rehovot Israel Univ Massachusetts Dept Microbiol Amherst MA 01003 USA Weizmann Inst Sci Dept Neurobiol IL-76100 Rehovot Israel Univ Maryland Inst Biotechnol Ctr Adv Res Biotechnol Rockville MD 20850 USA Weizmann Inst Sci Dept Biol Struct IL-76100 Rehovot Israel

Many scientists lack the background to fully utilize the wealth of solved three-dimensional biomacromolecule structures. Thus, a resource is needed to present structure/function information in a user-friendly manner to a broad scientific audience. Proteopedia http://*** is an interactive, wiki web-resource whose pages have embedded threedimensional structures surrounded by descriptive text containing hyperlinks that change the appearance (view, representations, colors, labels) of the adjacent three-dimensional structure to reflect the concept explained in the text.

关键词： protein data bank Structural Biology Authoring Tool Myristoyl protein data bank file

来源：评论

学校读者我要写书评

暂无评论

Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments

引用

GENOME BIOLOGY 2008年第3期9卷 R52-R52页

作者： Karuppasamy, Manikandan Pal, Debnath Suryanarayanarao, Ramakumar Brener, Nathan E. Iyengar, Sitharama S. Seetharaman, Guna Indian Inst Sci Bioinformat Ctr Bangalore 560012 Karnataka India Indian Inst Sci Dept Phys Bangalore 560012 Karnataka India Indian Inst Sci Supercomp Educ & Res Ctr Bangalore 560012 Karnataka India Louisiana State Univ Dept Comp Sci Baton Rouge LA 70803 USA

We have developed a geometric clustering algorithm using backbone phi,psi angles to group conformationally similar peptide fragments of any length. By labelling each fragment in the cluster with level-specific Gene Ontology molecular function (MF) term of its protein, we are able to compute statistics for MF-propensity and p-value of individual fragments in the cluster. Clustering-cum-statistical analysis for 8-length-trans-peptide fragments shows MF-propensities >= 20 and p-values <= 0.05 can dissect fragments within a protein linked to the MF.

关键词： Gene Ontology protein data bank Additional data file protein data bank file protein data bank Entry

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：