Literature DB >> 11836236

PCSB--a program collection for structural biology and biophysical chemistry.

A Hofmann1, A Wlodawer.   

Abstract

We present the first package of Java classes specifically aimed at the handling of structural and biophysical problems. To enable object-oriented programming a basis of fundamental Java classes is required which deals with basic operations of vectors, matrices, amino acid sequences, crystal symmetries and PDB files. Five classes, which carry out these basic operations, were constructed and bundled together with several utility functions in the PCSB package. Furthermore, to demonstrate their applicability and to obtain programs handling common tasks in structural laboratories, we present the first six applications of PCSB. All applications are portable to different platforms and require only the Java Runtime Environment to be installed on the system. available as PDF file.

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Year:  2002        PMID: 11836236     DOI: 10.1093/bioinformatics/18.1.209

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


  9 in total

1.  Expression, purification and preliminary crystallographic analysis of the recombinant β-glucosidase (BglA) from the halothermophile Halothermothrix orenii.

Authors:  Lokesh D Kori; Andreas Hofmann; Bharat K C Patel
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-12-23

2.  Membrane-induced folding and structure of membrane-bound annexin A1 N-terminal peptides: implications for annexin-induced membrane aggregation.

Authors:  Nien-Jen Hu; Jeremy Bradshaw; Hans Lauter; Julia Buckingham; Egle Solito; Andreas Hofmann
Journal:  Biophys J       Date:  2007-11-09       Impact factor: 4.033

3.  SDAR: a practical tool for graphical analysis of two-dimensional data.

Authors:  Saroja Weeratunga; Nien-Jen Hu; Anne Simon; Andreas Hofmann
Journal:  BMC Bioinformatics       Date:  2012-08-14       Impact factor: 3.169

4.  Insights into the membrane interactions of the saposin-like proteins Na-SLP-1 and Ac-SLP-1 from human and dog hookworm.

Authors:  Charlene Willis; Conan K Wang; Asiah Osman; Anne Simon; Darren Pickering; Jason Mulvenna; Alan Riboldi-Tunicliffe; Malcolm K Jones; Alex Loukas; Andreas Hofmann
Journal:  PLoS One       Date:  2011-10-03       Impact factor: 3.240

5.  Divalent cations and redox conditions regulate the molecular structure and function of visinin-like protein-1.

Authors:  Conan K Wang; Anne Simon; Christian M Jessen; Cristiano L P Oliveira; Lynsey Mack; Karl-Heinz Braunewell; James B Ames; Jan Skov Pedersen; Andreas Hofmann
Journal:  PLoS One       Date:  2011-11-02       Impact factor: 3.240

6.  Phosphorylation of CRN2 by CK2 regulates F-actin and Arp2/3 interaction and inhibits cell migration.

Authors:  Charles-Peter Xavier; Raphael H Rastetter; Margit Blömacher; Maria Stumpf; Mirko Himmel; Reginald O Morgan; Maria-Pilar Fernandez; Conan Wang; Asiah Osman; Yoshihiko Miyata; Ruth A Gjerset; Ludwig Eichinger; Andreas Hofmann; Stefan Linder; Angelika A Noegel; Christoph S Clemen
Journal:  Sci Rep       Date:  2012-01-31       Impact factor: 4.379

7.  An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements.

Authors:  Conan K Wang; Andreas Hofmann
Journal:  3 Biotech       Date:  2014-05-20       Impact factor: 2.406

8.  A practical Java tool for small-molecule compound appraisal.

Authors:  Parisa Amani; Todd Sneyd; Sarah Preston; Neil D Young; Lyndel Mason; Ulla-Maja Bailey; Jonathan Baell; David Camp; Robin B Gasser; Alain-Dominique Gorse; Paul Taylor; Andreas Hofmann
Journal:  J Cheminform       Date:  2015-06-16       Impact factor: 5.514

9.  Flatworms have lost the right open reading frame kinase 3 gene during evolution.

Authors:  Bert Breugelmans; Brendan R E Ansell; Neil D Young; Parisa Amani; Andreas J Stroehlein; Paul W Sternberg; Aaron R Jex; Peter R Boag; Andreas Hofmann; Robin B Gasser
Journal:  Sci Rep       Date:  2015-05-15       Impact factor: 4.379

  9 in total

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