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Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins

Kuan Pern Tan, Thanh Binh Nguyen, Siddharth Patel, Raghavan Varadarajan, M. S. Madhusudhan
2013 Nucleic Acids Research  
Some of the cavities identified are capable of binding small molecule ligands. In this study, we have enhanced our depth-based predictions of binding sites by including evolutionary information.  ...  Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water.  ...  ACKNOWLEDGEMENTS The authors thank Yong Taipang for his support in the setting up and maintenance of the web server.  ... 
doi:10.1093/nar/gkt503 pmid:23766289 pmcid:PMC3692129 fatcat:wci2jqlmwnczfiovkfjztma7ly

Two Complementary Methods for Relative Quantification of Ligand Binding Site Burial Depth in Proteins: The "Cutting Plane" and "Tangent Sphere" Methods [article]

Vicente M. Reyes
2015 arXiv   pre-print
We describe two complementary methods to quantify the degree of burial of ligand and/or ligand binding site (LBS) in a protein-ligand complex, namely, the "cutting plane" (CP) and the "tangent sphere"  ...  LBS burial depth is an important parameter as it is usually directly related to the amount of conformational change a protein undergoes upon ligand binding, and ability to quantify it could allow meaningful  ...  This work was supported by an Institutional Research and Academic Career Development  ... 
arXiv:1505.01142v1 fatcat:qznfsp3gavcf5d7o7fmcdpis5u

Combining Information from Crosslinks and Monolinks in the Modelling of Protein Structures [article]

Matthew Sinnott, Sony Malhotra, Mallur S Madhusudhan, Konstantinos Thalassinos, Maya Topf
2020 bioRxiv   pre-print
They convey residue exposure information, but so far have not been used in the modelling of protein structures.  ...  Here we present the Monolink Depth Score (MoDS), for assessing structural models based on the depth of monolinked residues, corresponding to their distance to the nearest bulk water.  ...  The copyright holder for this preprint this version posted . . https://doi.org/10.1101 to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable  ... 
doi:10.1101/2020.03.25.007104 fatcat:gafibi23gbbr7hwiodxtuxoryu

In silico approach in reveal traditional medicine plants pharmacological material basis

Fan Yi, Li Li, Li-jia Xu, Hong Meng, Yin-mao Dong, Hai-bo Liu, Pei-gen Xiao
2018 Chinese Medicine  
As computer technology has developed, in silico approaches such as virtual screening and network analysis have been widely utilized in efforts to elucidate the pharmacological basis of the functions of  ...  Furthermore, we conclude with a simple example that illustrates the whole methodology, and we present perspectives on the development and application of this in silico methodology to reveal the pharmacological  ...  Acknowledgements We very grateful to Pr. Jun Xu (Research Centerfor Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou) for his valuable suggestions.  ... 
doi:10.1186/s13020-018-0190-0 pmid:29946351 pmcid:PMC6006786 fatcat:btf7nau2wbeyrkrgxvuvvkn26i

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
Finally we want to thank to Prof. Wigley for the contribution to this work with the x-ray structure of the protein ligand to the GR1222222.  ...  effective binding in the kinase.  ...  In this study we have characterised and mapped ligand-binding cavities of proteins based on principal component analysis of cavity properties (related mainly to size, shape, polarity and charge), without  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

Fortieth Annual Meeting February 17-21, 1996 Baltimore Convention Center Baltimore, Maryland. Monday Symposia and Posters, Part IV

1996 Biophysical Journal  
We have expressed the recombinant proteins in Xenopus oocytes and have compared their water fluxing properties to MIP and Aquaporin-1, a known water channel.  ...  MIP-related proteins (MRPs) are a relatively new growing family of integral membrane proteins. MRPs are found in diverse phyla from man to archaebacteria.  ...  Bimolecular binding processes are ubiquitous in the biological sciences and the ability to compute absolute binding constants has implications for immunology, pharmacology, and rational drug design.  ... 
doi:10.1016/s0006-3495(96)79664-9 fatcat:cqlohnaop5bopinv32x36yk6ja

第54回年会予稿集

2016 Seibutsu Butsuri  
The pKa prediction of ionizable residues in proteins is a critical issue to reveal the atomistic mechanism of protein functions.  ...  The pKa values of two ionizable residues, D52 and E35, in hen egg white lysozyme were predicted by this method.  ...  3Pos313 Ohashi, Kaoru (大橋 郁) 3Pos279 3Pos284 Ohba, Yasunori (大庭 裕範) 3Pos065 Ohba, Yusuke (大場 雄介) 3SAA-03 Ohgita, Takashi (扇田 隆司) 3Pos072 Ohira, Ayaka (大平 彩花) 1Pos257 Ohki, Mio (大木 規央) 3Pos076 Ohkoshi, A.  ... 
doi:10.2142/biophys.56.s1 fatcat:jxxuc3tfpbhc5isjcmprzec2gi

Award Winners and Abstracts of the 31st Annual Symposium of The Protein Society, Montreal, Canada, July 24-27, 2017

2017 Protein Science  
In the present study, we aimed to improve the ExM method for imaging of proteins in human clinical tissue samples, for diagnostic pathology and research.  ...  limited to a 250nm resolution).  ...  Computational studies are of great interest to describe the folding/unfolding properties of proteins and to explain the interaction properties with other proteins or small ligands which can be used in  ... 
doi:10.1002/pro.3349 pmid:29280217 fatcat:jrxtwzblare37gxsvc5szbwuhu

Glyco25, XXV International Symposium on Glycoconjugates

2019 Glycoconjugate Journal  
During this lecture, I will present the potentiality of carbohydrate-coated gold nanoparticles as synthetic multivalent tool to interrogate and investigate immunological properties of carbohydrates, especially  ...  Gold nanoparticles have been explored as a tool to study the molecular interactions between S. pneumoniae polysaccharides and the human immune system.  ...  Nevertheless, due to its high susceptibility to stress and diseases, the aquaculture of C. maraena is a difficult endeavour and more knowledge of its physiology is necessary.  ... 
doi:10.1007/s10719-019-09880-4 fatcat:xdbfh5xegbfpfhugf3tgzbirq4

Proceedings of the World Molecular Imaging Congress 2021, October 5-8, 2021: General Abstracts

2022 Molecular Imaging and Biology  
resolution parameters (to maximize SNR/CNR) and a corresponding number of iterations for each resolution subset are taken in turn.  ...  The method can be applied to clinical MRI images and will be crucial in order to facilitate diagnosis of tumor progression at the earliest stages.  ...  The nanocluster system with a high selectivity showed the potential for fluorescence imaging and the integrating of gold and MMAE demonstrated excellent concurrent chemotherapy-radiotherapy efficacy, which  ... 
doi:10.1007/s11307-021-01693-y pmid:34982365 pmcid:PMC8725635 fatcat:4sfb3isoyfdhfbiwxfr55gvqym

Synthetic Transformations of Ent-Kaurenoic Acid

Olga Morarescu
2015 Chemistry Journal of Moldova: General, Industrial and Ecological Chemistry  
These calculations show that the transition of the protein from a conformation to another one is accompanied by changes in the protonation state of specific amino acid residues.  ...  The cyano-group of ligand is not coordinated to the lanthanide ion. This article is dedicated to the memory of Prof.  ...  The authors have to decide acknowledgement of certain collaborators, funds or programs who contributed in a way to the research described in the paper.  ... 
doi:10.19261/cjm.2015.10(1).01 fatcat:6gaegfaygfhavamgipxseluomy

Radiation vs Nuclear Size [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
After ligand binding, SOS attaches to the adaptor protein Grb2 containing an SH3 domain and through the SH2 domain of Grb2 the complex binds to the phospho- tyrosine residues of the signal receptor.  ...  Also, the binding proteins may attract other molecules that act in an activating or silencing manner. In an absolutely abstract form this may be visualized with a few computer symbols.  ...  The switching results in the generation of an 11-amino residue at the carboxyl end that destines the protein for degradation.  ... 
doi:10.1007/978-1-4020-6754-9_14032 fatcat:sjsarml6jbh37bxjg25tyvucga

Pelger(-Huet) Anomaly [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Ionizing radiation damage to the ataxia telangiectasia protein results in the phosphorylation of the serine 15 residue of p53 and checkpoint 2 (CHK2), which in turn phosphorylates residue 20.  ...  ▶protein kinases PKD: ▶polycystic kidney disease PKI (protein kinase I): A small protein, which attaches to the catalytic subunits of the heterotetrameric PKA and, with the aid of its nuclear localization  ...  The latter type of conformation is frequently found in internal regions of enzyme proteins and in structural protein elements such as silk fibers and collagen.  ... 
doi:10.1007/978-1-4020-6754-9_12490 fatcat:htaav6px6zcbbfuhaastehriru

Patristic Distance [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Ionizing radiation damage to the ataxia telangiectasia protein results in the phosphorylation of the serine 15 residue of p53 and checkpoint 2 (CHK2), which in turn phosphorylates residue 20.  ...  ▶protein kinases PKD: ▶polycystic kidney disease PKI (protein kinase I): A small protein, which attaches to the catalytic subunits of the heterotetrameric PKA and, with the aid of its nuclear localization  ...  The latter type of conformation is frequently found in internal regions of enzyme proteins and in structural protein elements such as silk fibers and collagen.  ... 
doi:10.1007/978-1-4020-6754-9_12406 fatcat:3qmewhcngva3tg4xf3ople4hxi

PMF (peptide-mass fingerprinting) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Ionizing radiation damage to the ataxia telangiectasia protein results in the phosphorylation of the serine 15 residue of p53 and checkpoint 2 (CHK2), which in turn phosphorylates residue 20.  ...  ▶protein kinases PKD: ▶polycystic kidney disease PKI (protein kinase I): A small protein, which attaches to the catalytic subunits of the heterotetrameric PKA and, with the aid of its nuclear localization  ...  The latter type of conformation is frequently found in internal regions of enzyme proteins and in structural protein elements such as silk fibers and collagen.  ... 
doi:10.1007/978-1-4020-6754-9_13064 fatcat:pzr5w5d5tvbyte6vp2kh3unfhe
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