共查询到20条相似文献,搜索用时 15 毫秒
1.
Background
The G-protein coupled receptor (GPCR) superfamily is currently the largest class of therapeutic targets. In silico prediction of interactions between GPCRs and small molecules in the transmembrane ligand-binding site is therefore a crucial step in the drug discovery process, which remains a daunting task due to the difficulty to characterize the 3D structure of most GPCRs, and to the limited amount of known ligands for some members of the superfamily. Chemogenomics, which attempts to characterize interactions between all members of a target class and all small molecules simultaneously, has recently been proposed as an interesting alternative to traditional docking or ligand-based virtual screening strategies. 相似文献2.
Chromato-panning: an efficient new mode of identifying suitable ligands from phage display libraries
Wim Noppe Fatima Plieva Igor Yu Galaev Hans Pottel Hans Deckmyn Bo Mattiasson 《BMC biotechnology》2009,9(1):21-9
Background
Phage Display technology is a well established technique for high throughput screening of affinity ligands. Here we describe a new compact chromato-panning procedure for selection of suitable binders from a phage peptide display library. 相似文献3.
Sampali Banerjee Jitendra Kumar Anjali Apte-Deshpande Sriram Padmanabhan 《Microbial cell factories》2010,9(1):30
Background
The selection of bacterial recombinants that harbour a desired insert, has been a key factor in molecular cloning and a series of screening procedures need to be performed for selection of clones carrying the genes of interest. The conventional cloning techniques are reported to have problems such as screening high number of colonies, generation of false positives, setting up of control ligation mix with vector alone etc. 相似文献4.
Shuxing Zhang Kamal Kumar Xiaohui Jiang Anders Wallqvist Jaques Reifman 《BMC bioinformatics》2008,9(1):126
Background
Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. 相似文献5.
6.
Background
The need for fast and accurate scoring functions has been driven by the increased use of in silico virtual screening twinned with high-throughput screening as a method to rapidly identify potential candidates in the early stages of drug development. We examine the ability of some the most common scoring functions (GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus) to discriminate correctly and efficiently between active and non-active compounds among a library of ~3,600 diverse decoy compounds in a virtual screening experiment against heat shock protein 90 (Hsp90). 相似文献7.
Background
The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. 相似文献8.
Background
Since a milestone work on Neisseria meningitidis B, Reverse Vaccinology has strongly enhanced the identification of vaccine candidates by replacing several experimental tasks using in silico prediction steps. These steps have allowed scientists to face the selection of antigens from the predicted proteome of pathogens, for which cell culture is difficult or impossible, saving time and money. However, this good example of bioinformatics-driven immunology can be further developed by improving in silico steps and implementing biologist-friendly tools. 相似文献9.
F. Puspasari O.K. Radjasa A.S. Noer Z. Nurachman Y.M. Syah M. van der Maarel L. Dijkhuizen Š. Janeček D. Natalia 《Journal of applied microbiology》2013,114(1):108-120
Aims
The aims were to isolate a raw starch–degrading α‐amylase gene baqA from Bacillus aquimaris MKSC 6.2, and to characterize the gene product through in silico study and its expression in Escherichia coli.Methods and Results
A 1539 complete open reading frame of a starch–degrading α‐amylase gene baqA from B. aquimaris MKSC 6·2 has been determined by employing PCR and inverse PCR techniques. Bioinformatics analysis revealed that B. aquimaris MKSC 6.2 α‐amylase (BaqA) has no starch‐binding domain, and together with a few putative α‐amylases from bacilli may establish a novel GH13 subfamily most closely related to GH13_1. Two consecutive tryptophans (Trp201 and Trp202, BaqA numbering) were identified as a sequence fingerprint of this novel GH13 subfamily. Escherichia coli cells produced the recombinant BaqA protein as inclusion bodies. The refolded recombinant BaqA protein degraded raw cassava and corn starches, but exhibited no activity with soluble starch.Conclusions
A novel raw starch–degrading B. aquimaris MKSC 6.2 α‐amylase BaqA is proposed to be a member of new GH13 subfamily.Significance and Impact of the Study
This study has contributed to the overall knowledge and understanding of amylolytic enzymes that are able to bind and digest raw starch directly. 相似文献10.
Young-Il Kim Taewoo Ryu Judong Lee Young-Shin Heo Joohong Ahnn Seung-Jae Lee OokJoon Yoo 《BMC cell biology》2010,11(1):9
Background
Caspases are cysteine proteases with essential functions in the apoptotic pathway; their proteolytic activity toward various substrates is associated with the morphological changes of cells. Recent reports have described non-apoptotic functions of caspases, including autophagy. In this report, we searched for novel modifiers of the phenotype of Dcp-1 gain-of-function (GF) animals by screening promoter element- inserted Drosophila melanogaster lines (EP lines). 相似文献11.
Ali Al-Shahib Raju Misra Nadia Ahmod Min Fang Haroun Shah Saheer Gharbia 《BMC bioinformatics》2010,11(1):437
Background
Robust biomarkers are needed to improve microbial identification and diagnostics. Proteomics methods based on mass spectrometry can be used for the discovery of novel biomarkers through their high sensitivity and specificity. However, there has been a lack of a coherent pipeline connecting biomarker discovery with established approaches for evaluation and validation. We propose such a pipeline that uses in silico methods for refined biomarker discovery and confirmation. 相似文献12.
Adnane Sellam Hervé Hogues Christopher Askew Faiza Tebbji Marco van het Hoog Hugo Lavoie Carol A Kumamoto Malcolm Whiteway André Nantel 《Genome biology》2010,11(7):R71
Background
Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. 相似文献13.
Bevan KS Chung Suresh Selvarasu Andrea Camattari Jimyoung Ryu Hyeokweon Lee Jungoh Ahn Hongweon Lee Dong-Yup Lee 《Microbial cell factories》2010,9(1):50
Background
Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism. 相似文献14.
Background
A growing number of realistic in silico models of metabolic functions are being formulated and can serve as 'dry lab' platforms to prototype and simulate experiments before they are performed. For example, dual perturbation experiments that vary both genetic and environmental parameters can readily be simulated in silico. Genetic and environmental perturbations were applied to a cell-scale model of the human erythrocyte and subsequently investigated. 相似文献15.
Stefan Günther Christian Senger Elke Michalsky Andrean Goede Robert Preissner 《BMC bioinformatics》2006,7(1):293
Background
The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of ligands is a critical point for the selection of potential drugs. Since computed 3D structures of millions of compounds are available, the knowledge of their binding conformations would be a great benefit for the development of efficient screening methods. 相似文献16.
Olfa Frikha-Gargouri Radhouane Gdoura Abir Znazen Boutheina Gargouri Jalel Gargouri Ahmed Rebai Adnene Hammami 《BMC microbiology》2008,8(1):217
Background
The OmcB protein is one of the most immunogenic proteins in C. trachomatis and C. pneumoniae infections. This protein is highly conserved leading to serum cross reactivity between the various chlamydial species. Since previous studies based on recombinant proteins failed to identify a species specific immune response against the OmcB protein, this study evaluated an in silico predicted specific and immunogenic antigen from the OmcB protein for the serodiagnosis of C. trachomatis infections. 相似文献17.
Rebecca F Halperin Phillip Stafford Jack S Emery Krupa Arun Navalkar Stephen Albert Johnston 《BMC bioinformatics》2012,13(1):1
Background
Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. 相似文献18.
Background
An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species. 相似文献19.
Konstantinos P Exarchos Themis P Exarchos Georgios Rigas Costas Papaloukas Dimitrios I Fotiadis 《BMC bioinformatics》2011,12(1):142