Literature DB >> 16407320

BioShell--a package of tools for structural biology computations.

Dominik Gront1, Andrzej Kolinski.   

Abstract

SUMMARY: BioShell is a suite of programs performing common tasks accompanying protein structure modeling. BioShell design is based on UNIX shell flexibility and should be used as its extension. Using BioShell various molecular modeling procedures can be integrated in a single pipeline. AVAILABILITY: BioShell package can be downloaded from its website http://biocomp.chem.uw.edu.pl/BioShell and these pages provide many examples and a detailed documentation for the newest version.

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Year:  2006        PMID： 16407320     DOI： 10.1093/bioinformatics/btk037

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


  24 in total

1.  Molecular determinants for antibody binding on group 1 house dust mite allergens.

Authors:  Maksymilian Chruszcz; Anna Pomés; Jill Glesner; Lisa D Vailes; Tomasz Osinski; Przemyslaw J Porebski; Karolina A Majorek; Peter W Heymann; Thomas A E Platts-Mills; Wladek Minor; Martin D Chapman
Journal:  J Biol Chem       Date:  2011-12-30       Impact factor: 5.157

2.  Structural Basis for the Interaction of a Human Small Heat Shock Protein with the 14-3-3 Universal Signaling Regulator.

Authors:  Nikolai N Sluchanko; Steven Beelen; Alexandra A Kulikova; Stephen D Weeks; Alfred A Antson; Nikolai B Gusev; Sergei V Strelkov
Journal:  Structure       Date:  2017-01-12       Impact factor: 5.006

3.  Folding pathway of the b1 domain of protein G explored by multiscale modeling.

Authors:  Sebastian Kmiecik; Andrzej Kolinski
Journal:  Biophys J       Date:  2007-09-21       Impact factor: 4.033

4.  Characterization of protein-folding pathways by reduced-space modeling.

Authors:  Sebastian Kmiecik; Andrzej Kolinski
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-16       Impact factor: 11.205

5.  Fast and accurate methods for predicting short-range constraints in protein models.

Authors:  Dominik Gront; Andrzej Kolinski
Journal:  J Comput Aided Mol Des       Date:  2008-04-15       Impact factor: 3.686

6.  The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.

Authors:  Shuren Wang; Olga Kirillova; Maksymilian Chruszcz; Dominik Gront; Matthew D Zimmerman; Marcin T Cymborowski; Igor A Shumilin; Tatiana Skarina; Elena Gorodichtchenskaia; Alexei Savchenko; Aled M Edwards; Wladek Minor
Journal:  Protein Sci       Date:  2009-11       Impact factor: 6.725

7.  Structural analysis of a putative aminoglycoside N-acetyltransferase from Bacillus anthracis.

Authors:  Maria M Klimecka; Maksymilian Chruszcz; Jose Font; Tatiana Skarina; Igor Shumilin; Olena Onopryienko; Przemyslaw J Porebski; Marcin Cymborowski; Matthew D Zimmerman; Jeremy Hasseman; Ian J Glomski; Lukasz Lebioda; Alexei Savchenko; Aled Edwards; Wladek Minor
Journal:  J Mol Biol       Date:  2011-05-13       Impact factor: 5.469

8.  When the lowest energy does not induce native structures: parallel minimization of multi-energy values by hybridizing searching intelligences.

Authors:  Qiang Lü; Xiao-Yan Xia; Rong Chen; Da-Jun Miao; Sha-Sha Chen; Li-Jun Quan; Hai-Ou Li
Journal:  PLoS One       Date:  2012-09-28       Impact factor: 3.240

9.  Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid.

Authors:  Mateusz Kurcinski; Andrzej Kolinski
Journal:  J Steroid Biochem Mol Biol       Date:  2010-04-14       Impact factor: 4.292

10.  Detecting local residue environment similarity for recognizing near-native structure models.

Authors:  Hyungrae Kim; Daisuke Kihara
Journal:  Proteins       Date:  2014-10-30
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