Literature DB >> 19244385

PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes.

Timothy V Pyrkov1, Anton O Chugunov, Nikolay A Krylov, Dmitry E Nolde, Roman G Efremov.   

Abstract

UNLABELLED: The PLATINUM (Protein-Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP). AVAILABILITY: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Year:  2009        PMID： 19244385     DOI： 10.1093/bioinformatics/btp111

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  54 in total

1.  Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels.

Authors:  Eric Hajjar; Amit Kumar; Paolo Ruggerone; Matteo Ceccarelli
Journal:  J Mol Model       Date:  2010-11       Impact factor: 1.810

2.  Structural Insight into Specificity of Interactions between Nonconventional Three-finger Weak Toxin from Naja kaouthia (WTX) and Muscarinic Acetylcholine Receptors.

Authors:  Ekaterina N Lyukmanova; Zakhar O Shenkarev; Mikhail A Shulepko; Alexander S Paramonov; Anton O Chugunov; Helena Janickova; Eva Dolejsi; Vladimir Dolezal; Yuri N Utkin; Victor I Tsetlin; Alexander S Arseniev; Roman G Efremov; Dmitry A Dolgikh; Mikhail P Kirpichnikov
Journal:  J Biol Chem       Date:  2015-08-04       Impact factor: 5.157

Review 3.  Latarcins: versatile spider venom peptides.

Authors:  Peter V Dubovskii; Alexander A Vassilevski; Sergey A Kozlov; Alexey V Feofanov; Eugene V Grishin; Roman G Efremov
Journal:  Cell Mol Life Sci       Date:  2015-08-19       Impact factor: 9.261

4.  Heterodimeric Insecticidal Peptide Provides New Insights into the Molecular and Functional Diversity of Ant Venoms.

Authors:  Axel Touchard; Helen C Mendel; Isabelle Boulogne; Volker Herzig; Nayara Braga Emidio; Glenn F King; Mathilde Triquigneaux; Lucie Jaquillard; Rémy Beroud; Michel De Waard; Olivier Delalande; Alain Dejean; Markus Muttenthaler; Christophe Duplais
Journal:  ACS Pharmacol Transl Sci       Date:  2020-10-06

5.  How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case.

Authors:  Landry Charlier; Jérémie Topin; Catherine Ronin; Soo-Kyung Kim; William A Goddard; Roman Efremov; Jérôme Golebiowski
Journal:  Cell Mol Life Sci       Date:  2012-08-29       Impact factor: 9.261

6.  Complexes of Peptide Blockers with Kv1.6 Pore Domain: Molecular Modeling and Studies with KcsA-Kv1.6 Channel.

Authors:  O V Nekrasova; A D Volyntseva; K S Kudryashova; V N Novoseletsky; E A Lyapina; A V Illarionova; S A Yakimov; Yu V Korolkova; K V Shaitan; M P Kirpichnikov; A V Feofanov
Journal:  J Neuroimmune Pharmacol       Date:  2016-09-17       Impact factor: 4.147

7.  Fine mapping of hydrophobic contacts reassesses the organization of the first three dystrophin coiled-coil repeats.

Authors:  Dominique Mias-Lucquin; Angélique Chéron; Elisabeth Le Rumeur; Jean-François Hubert; Olivier Delalande
Journal:  Protein Sci       Date:  2019-01-14       Impact factor: 6.725

8.  Structural Basis of Neuronal Nitric-oxide Synthase Interaction with Dystrophin Repeats 16 and 17.

Authors:  Anne-Elisabeth Molza; Khushdeep Mangat; Elisabeth Le Rumeur; Jean-François Hubert; Nick Menhart; Olivier Delalande
Journal:  J Biol Chem       Date:  2015-09-16       Impact factor: 5.157

9.  Structural Basis for Human Norovirus Capsid Binding to Bile Acids.

Authors:  Turgay Kilic; Anna Koromyslova; Grant S Hansman
Journal:  J Virol       Date:  2019-01-04       Impact factor: 5.103

10.  Versatility of non-native forms of human cytochrome c: pH and micellar concentration dependence.

Authors:  Matthieu Simon; Valérie Metzinger-Le Meuth; Soizic Chevance; Olivier Delalande; Arnaud Bondon
Journal:  J Biol Inorg Chem       Date:  2012-10-16       Impact factor: 3.358
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