Literature DB >> 12824316

VADAR: a web server for quantitative evaluation of protein structure quality.

Leigh Willard1, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F Boyko, Brian D Sykes, David S Wishart.   

Abstract

VADAR (Volume Area Dihedral Angle Reporter) is a comprehensive web server for quantitative protein structure evaluation. It accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input and calculates, identifies, graphs, reports and/or evaluates a large number (>30) of key structural parameters both for individual residues and for the entire protein. These include excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality. These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar.

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Year:  2003        PMID： 12824316      PMCID： PMC168972          DOI： 10.1093/nar/gkg565

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  16 in total

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Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

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Journal:  J Mol Biol       Date:  1978-03-25       Impact factor: 5.469
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  275 in total

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Authors:  Rajarshi Maiti; Gary H Van Domselaar; Haiyan Zhang; David S Wishart
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids.

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Journal:  J Biomol NMR       Date:  2011-10-30       Impact factor: 2.835

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4.  Mutational and cysteine scanning analysis of the glucagon receptor N-terminal domain.

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Journal:  J Biol Chem       Date:  2010-07-20       Impact factor: 5.157

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Authors:  Navneet Phogat; Vaibhav Vindal; Vikash Kumar; Krishna K Inampudi; Nirmal K Prasad
Journal:  J Mol Model       Date:  2010-02-19       Impact factor: 1.810

6.  Mapping surface accessibility of the C1r/C1s tetramer by chemical modification and mass spectrometry provides new insights into assembly of the human C1 complex.

Authors:  Sébastien Brier; Delphine Pflieger; Maxime Le Mignon; Isabelle Bally; Christine Gaboriaud; Gérard J Arlaud; Régis Daniel
Journal:  J Biol Chem       Date:  2010-06-30       Impact factor: 5.157

7.  In silico characterization of thermostable lipases.

Authors:  Debamitra Chakravorty; Saravanan Parameswaran; Vikash Kumar Dubey; Sanjukta Patra
Journal:  Extremophiles       Date:  2010-12-12       Impact factor: 2.395

8.  Using a low denaturant model to explore the conformational features of translocation-active SecA.

Authors:  Jenny L Maki; Beena Krishnan; Lila M Gierasch
Journal:  Biochemistry       Date:  2012-02-08       Impact factor: 3.162

9.  Molecular characterization, modeling, in silico analysis of equine pituitary gonadotropin alpha subunit and docking interaction studies with ganirelix.

Authors:  Anuradha Bhardwaj; Varij Nayan; Parvati Sharma; Sanjay Kumar; Yash Pal; Jitender Singh
Journal:  In Silico Pharmacol       Date:  2017-07-18

10.  Limits to Compensatory Mutations: Insights from Temperature-Sensitive Alleles.

Authors:  Katarzyna Tomala; Piotr Zrebiec; Daniel L Hartl
Journal:  Mol Biol Evol       Date:  2019-09-01       Impact factor: 16.240
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