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structural bioinformatics analysis of free cysteines in protein environments

JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS 2009年第2期40卷 123-129页

作者： Ho, Sheau Ling Wang, Andrew H. -J. Chinese Culture Univ Dept Chem Engn Taipei 111 Taiwan Acad Sinica Inst Biol Chem Taipei 115 Taiwan

Cysteine has been considered as a "hydrophilic" amino acid because of its pK(a) and its ability to form (weak)hydrogen bonds. However, cysteines are found mostly in hydrophobic environments, either in S-S (disulphide) form or in free cysteine form. When free cysteines are found on the surface of proteins, they are often involved in catalytic residues, as in cysteine proteases, P-loop phosphatases, etc. Additionally, a unique property of cysteines is that their side-chain volume is different from all other amino acids. This study is focused on the discrimination between structural versus active free cysteines based on a local environment analysis which does not appear to have been attempted previously. We have demonstrated the corresponding structural positions associated with free cysteines in their three-dimensional localization environment We examined protein samples including nine, sequenced, coronavirus proteases and cysteine-rich non-membrane proteins. Our present study shows that the sequential environments of free cysteines of coronavirus proteases are rather hydrophobic and that the free cysteines of non-membrane proteases have a higher amount of contacts to hydrophobic residues and lower amount of contacts to polar or charged residues. (C) 2008 Taiwan Institute of Chemical Engineers. Published by Elsevier B.V. All rights reserved.

关键词： Hydrophobic Free cysteine SH SS Proteases Spatial neighborhood structural preference structural bioinformatics

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structural bioinformatics study of PNP from Schistosoma mansoni

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2004年第1期322卷 100-104页

作者： da Silveira, NJF Uchôa, HB Canduri, F Pereira, JH Camera, JC Basso, LA Palma, MS Santos, DS de Azevedo, WF Pontificia Univ Catolica Rio Grande do Sul Ctr Res & Dev Mol Struct & Funct Mol Biol BR-90619900 Porto Alegre RS Brazil UNESP Dept Phys BR-15054000 Sao Jose Do Rio Preto SP Brazil Univ Fed Rio Grande do Sul Dept Mol Biol & Biotechnol Rede Brasileira Pesquisas TB BR-91501970 Porto Alegre RS Brazil UNESP Inst Biosci Dept Biol Lab Struct Biol & Zoochem BR-13506900 Rio Claro SP Brazil Univ Estadual Paulista Inst Biosci Dept Biol Lab Struct Biol & Zoochem BR-05503900 Sao Paulo Brazil Inst Butantan Ctr Appl Toxicol BR-05503900 Sao Paulo Brazil

The parasite Schistosoma mansoni lacks the de novo pathway for purine biosynthesis and depends on salvage pathways for its purine requirements. Schistosomiasis is endemic in 76 countries and territories and amongst the parasitic diseases ranks second after malaria in terms of social and economic impact and public health importance. The PNP is an attractive target for drug design and it has been submitted to extensive structure-based design. The atomic coordinates of the complex of human PNP with inosine were used as template for starting the modeling of PNP from S. mansoni complexed with inosine. Here we describe the model for the complex SmPNP-inosine and correlate the structure with differences in the affinity for inosine presented by human and S. mansoni PNPs. (C) 2004 Elsevier Inc. All rights reserved.

关键词： structural bioinformatics Schistosoma mansoni PNP drug design

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structural bioinformatics TOOLS FOR THE COMPARISON AND CLASSIFICATION OF PROTEIN INTERACTIONS

STRUCTURAL BIOINFORMATICS TOOLS FOR THE COMPARISON AND CLASS...

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作者： Leonardo D. Garma University of Oulu

学位级别：博士

Most proteins carry out their functions through interactions with other molecules. Thus, proteins taking part in similar interactions are likely to carry out related functions. One way to determine whether two proteins do take part in similar interactions is by quantifying the likeness of their structures. This work focuses on the development of methods for the comparison of protein- protein and protein-ligand interactions, as well as their application to structure-based classification schemes. A method based on the MultiMer-align (or MM-align) program was developed and used to compare all known dimeric protein complexes. The results of the comparison demonstrates that the method improves over MM-align in a significant number of cases. The data was employed to classify the complexes, resulting in 1,761 different protein-protein interaction types. Through a statistical model, the number of existing protein-protein interaction types in nature was estimated at around 4,000. The model allowed the establishment of a relationship between the number of quaternary families (sequence-based groups of protein-protein complexes) and quaternary folds (structure-based groups). The interactions between proteins and small organic ligands were studied using sequence- independent methodologies. A new method was introduced to test three similarity metrics. The best of these metrics was subsequently employed, together with five other existing methodologies, to conduct an all-to-all comparison of all the known protein-FAD (Flavin-Adenine Dinucleotide) complexes. The results demonstrates that the new methodology captures the best the similarities between complexes in terms of protein-ligand contacts. Based on the all-to-all comparison, the protein-FAD complexes were subsequently separated into 237 groups. In the majority of cases, the classification divided the complexes according to their annotated function. Using a graph-based description of the FAD-binding sites, each group could be f

关键词： binding site comparison flavin adenine dinucleotide (FAD) protein-protein interactions structural alignment structural bioinformatics structural similarity

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A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins

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PROTEIN ENGINEERING DESIGN & SELECTION 2013年第4期26卷 283-289页

作者： Choi, Eun Jung Jacak, Ron Kuhlman, Brian Univ N Carolina Dept Biochem & Biophys Chapel Hill NC 27599 USA Univ N Carolina Lineberger Comprehens Canc Care Ctr Chapel Hill NC 27599 USA

We have developed a protocol for identifying proteins that are predisposed to bind linear epitopes on target proteins of interest. The protocol searches through the protein database for proteins (scaffolds) that are bound to peptides with sequences similar to accessible, linear epitopes on the target protein. The sequence match is considered more significant if residues calculated to be important in the scaffoldpeptide interaction are present in the target epitope. The crystal structure of the scaffoldpeptide complex is then used as a template for creating a model of the scaffold bound to the target epitope. This model can then be used in conjunction with sequence optimization algorithms or directed evolution methods to search for scaffold mutations that further increase affinity for the target protein. To test the applicability of this approach we targeted three disease-causing proteins: a tuberculosis virulence factor (TVF), the apical membrane antigen (AMA) from malaria, and hemagglutinin from influenza. In each case the best scoring scaffold was tested, and binders with K(d)s equal to 37 M and 50 nM for TVF and AMA, respectively, were identified. A web server () has been created for performing the scaffold search process with user-defined target sequences.

关键词： epitope protein engineering proteinprotein interaction protein scaffold structural bioinformatics

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Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics

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COMPUTATIONAL AND structural BIOTECHNOLOGY JOURNAL 2022年 20卷 117-127页

作者： Tripathi, Swarnendu Dsouza, Nikita R. Mathison, Angela J. Leverence, Elise Urrutia, Raul Zimmermann, Michael T. Med Coll Wisconsin Genom Sci & Precis Med Ctr GSPMC Bioinfomat Res & Dev Lab Milwaukee WI 53226 USA Med Coll Wisconsin Genom Sci & Precis Med Ctr GSPMC Milwaukee WI 53226 USA Med Coll Wisconsin Dept Surg Div Res Milwaukee WI 53226 USA Med Coll Wisconsin Clin & Translat Sci Inst Milwaukee WI 53226 USA Med Coll Wisconsin Dept Biochem Milwaukee WI 53226 USA St Jude Childrens Res Hosp Dept Struct Biol 332 N Lauderdale St Memphis TN 38105 USA

In the current study, we report computational scores for advancing genomic interpretation of disease-associated genomic variation in members of the RAS family of genes. For this purpose, we applied 31 sequence-and 3D structure-based computational scores, chosen by their breadth of biophysical properties. We parametrized our data by assembling a numerically homogenized experimentally-derived dataset, which when use in our calculations reveal that computational scores using 3D structure highly correlate with experimental measures (e.g., GAP-mediated hydrolysis R-Spearman = 0.80 and RAF affinity R-spearman = 0.82), while sequence-based scores are discordant with this data. Performing all-against-all comparisons, we applied this parametrized modeling approach to the study of 935 RAS variants from 7 RAS genes, which led us to identify 4 groups of mutations according to distinct biochemical scores within each group. Each group was comprised of hotspot and non-hotspot KRAS variants, indicating that poorly characterized variants could functionally behave like pathogenic mutations. Combining computational scores using dimensionality reduction indicated that changes to local unfolding propensity associate with changes in enzyme activity by genomic variants. Hence, our systematic approach, combining methodologies from both clinical genomics and 3D structural bioinformatics, represents an expansion for interpreting genomic data, provides information of mechanistic value, and that is transferable to other proteins. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and structural Biotechnology.

关键词： Genomics Protein science Data interpretation RAS mutation structural bioinformatics Functional genomics

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Constraint programming in structural bioinformatics

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CONSTRAINTS 2008年第1-2期13卷 3-20页

作者： Barahona, Pedro Krippahl, Ludwig Univ Nova Lisboa Dept Informat P-2825 Monte De Caparica Portugal

bioinformatics aims at applying computer science methods to the wealth of data collected in a variety of experiments in life sciences (e.g. cell and molecular biology, biochemistry, medicine, etc.) in order to help analysing such data and eliciting new knowledge from it. In addition to string processing bioinformatics is often identified with machine learning used for mining the large banks of bio-data available in electronic format, namely in a number of web servers. Nevertheless, there are opportunities of applying other computational techniques in some bioinformatics applications. In this paper, we report the application of constraint programming to address two structural bioinformatics problems, protein structure prediction and protein interaction (docking). The efficient application of constraint programming requires innovative modelling of these problems, as well as the development of advanced propagation techniques (e.g. global reasoning and propagation), which were adopted in Chemera, a system that is currently used to support biochemists in their research.

关键词： constraint programming structural bioinformatics protein structure determination protein docking

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A Single Sign-On Infrastructure for Science Gateways on a Use Case for structural bioinformatics

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JOURNAL OF GRID COMPUTING 2012年第4期10卷 769-790页

作者： Gesing, Sandra Grunzke, Richard Krueger, Jens Birkenheuer, Georg Wewior, Martin Schaefer, Patrick Schuller, Bernd Schuster, Johannes Herres-Pawlis, Sonja Breuers, Sebastian Balasko, Akos Kozlovszky, Miklos Fabri, Anna Szikszay Packschies, Lars Kacsuk, Peter Blunk, Dirk Steinke, Thomas Brinkmann, Andre Fels, Gregor Mueller-Pfefferkorn, Ralph Jaekel, Rene Kohlbacher, Oliver Univ Tubingen Tubingen Germany Tech Univ Dresden D-01062 Dresden Germany Univ Gesamthsch Paderborn Paderborn Germany Univ Cologne D-50931 Cologne Germany Konrad Zuse Zentrum Informat Tech Berlin Berlin Germany Forschungszentrum Julich D-52425 Julich Germany Univ Munich Munich Germany MTA SZTAKI Budapest Hungary Johannes Gutenberg Univ Mainz Mainz Germany

structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.

关键词： Single sign-on Science gateway Security DCIs structural bioinformatics

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Minireview: Applied structural bioinformatics in Proteomics

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PROTEIN JOURNAL 2013年第7期32卷 505-511页

作者： Choong, Yee Siew Tye, Gee Jun Lim, Theam Soon Univ Sains Malaysia Inst Res Mol Med INFORMM Minden 11800 Pulau Pinang Malaysia

The limited sequence similarity of protein sequences with known structures has led to an indispensable need for computational technology to predict their structures. structural bioinformatics (SB) has become integral in elucidating the sequence-structure-function relationship of a protein. This report focuses on the applications of SB within the context of protein engineering including its limitation and future challenges.

关键词： structural bioinformatics Structure-function relationship Protein-protein interaction networks Protein design

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p3d-Python module for structural bioinformatics

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BMC bioinformatics 2009年第1期10卷 1-5页

作者： Fufezan, Christian Specht, Michael Univ Munster Inst Evolut & Biodivers D-48149 Munster Germany Univ Munster Inst Biochem & Biotechnol Pflanzen D-48143 Munster Germany

Background: High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results: p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion: p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

关键词： Complex Query Vector Operation Plane Class Query Function structural bioinformatics

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NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology (vol 17, 62, 2016)

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BMC bioinformatics 2016年第4期17卷 211-214页

作者： Romano, Paolo Cordero, Francesca CBA IRCCS AOU San Martino IST Bioinformat Largo Rosanna Benzi 10 I-16132 Genoa Italy

The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology.43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this ***, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.

关键词： structural bioinformatics Tutorial Talk Integrative System Biology Keynote Talk Peer Review Procedure

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