Literature DB >> 14696386

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences.

Donald Petrey1, Barry Honig.   

Abstract

The widespread use of the original version of GRASP revealed the importance of the visualization of physicochemical and structural properties on the molecular surface. This chapter describes a new version of GRASP that contains many new capabilities. In terms of analysis tools, the most notable new features are sequence and structure analysis and alignment tools and the graphical integration of sequence and structural information. Not all the new GRASP2 could be described here and more capabilities are continually being added. An on-line manual, details on obtaining the software, and technical notes about the program and the Troll software library can be found at the Honig laboratory Web site (http://trantor.bioc.columbia.edu).

Entities:  

Mesh：

Substances：

Year:  2003        PMID： 14696386     DOI： 10.1016/S0076-6879(03)74021-X

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


  110 in total

1.  Differential geometry based solvation model II: Lagrangian formulation.

Authors:  Zhan Chen; Nathan A Baker; G W Wei
Journal:  J Math Biol       Date:  2011-01-30       Impact factor: 2.259

2.  Predicting transmembrane beta-barrels in proteomes.

Authors:  Henry R Bigelow; Donald S Petrey; Jinfeng Liu; Dariusz Przybylski; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2004-05-11       Impact factor: 16.971

3.  Helical packing patterns in membrane and soluble proteins.

Authors:  Marina Gimpelev; Lucy R Forrest; Diana Murray; Barry Honig
Journal:  Biophys J       Date:  2004-10-01       Impact factor: 4.033

4.  Electrostatic interactions between arginines and the minor groove in the nucleosome.

Authors:  Sean M West; Remo Rohs; Richard S Mann; Barry Honig
Journal:  J Biomol Struct Dyn       Date:  2010-06

5.  Protein interface conservation across structure space.

Authors:  Qiangfeng Cliff Zhang; Donald Petrey; Raquel Norel; Barry H Honig
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-01       Impact factor: 11.205

6.  Structure of Plasmodium falciparum ADP-ribosylation factor 1.

Authors:  William J Cook; Craig D Smith; Olga Senkovich; Anthony A Holder; Debasish Chattopadhyay
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-10-27

7.  Structure and function of APH(4)-Ia, a hygromycin B resistance enzyme.

Authors:  Peter J Stogios; Tushar Shakya; Elena Evdokimova; Alexei Savchenko; Gerard D Wright
Journal:  J Biol Chem       Date:  2010-11-17       Impact factor: 5.157

8.  In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor.

Authors:  Lin Wang; Shawn Witham; Zhe Zhang; Lin Li; Michael E Hodsdon; Emil Alexov
Journal:  Commun Comput Phys       Date:  2013-01       Impact factor: 3.246

9.  Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.

Authors:  Simon Arragain; Ricardo Garcia-Serres; Geneviève Blondin; Thierry Douki; Martin Clemancey; Jean-Marc Latour; Farhad Forouhar; Helen Neely; Gaetano T Montelione; John F Hunt; Etienne Mulliez; Marc Fontecave; Mohamed Atta
Journal:  J Biol Chem       Date:  2009-12-09       Impact factor: 5.157

10.  Structural templates for comparative protein docking.

Authors:  Ivan Anishchenko; Petras J Kundrotas; Alexander V Tuzikov; Ilya A Vakser
Journal:  Proteins       Date:  2015-06-13
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.