Literature DB >> 15215436

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

Matthias Heinig1, Dmitrij Frishman.   

Abstract

STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/.

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Year:  2004        PMID： 15215436      PMCID： PMC441567          DOI： 10.1093/nar/gkh429

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


  13 in total

1.  Continuum secondary structure captures protein flexibility.

Authors:  Claus A F Andersen; Arthur G Palmer; Søren Brunak; Burkhard Rost
Journal:  Structure       Date:  2002-02       Impact factor: 5.006

2.  The distribution and query systems of the RCSB Protein Data Bank.

Authors:  Philip E Bourne; Kenneth J Addess; Wolfgang F Bluhm; Li Chen; Nita Deshpande; Zukang Feng; Ward Fleri; Rachel Green; Jeffrey C Merino-Ott; Wayne Townsend-Merino; Helge Weissig; John Westbrook; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Authors:  Simon C Lovell; Ian W Davis; W Bryan Arendall; Paul I W de Bakker; J Michael Word; Michael G Prisant; Jane S Richardson; David C Richardson
Journal:  Proteins       Date:  2003-02-15

Review 4.  Secondary structure assignment.

Authors:  Claus A F Andersen; Burkhard Rost
Journal:  Methods Biochem Anal       Date:  2003

5.  PDBsum: a Web-based database of summaries and analyses of all PDB structures.

Authors:  R A Laskowski; E G Hutchinson; A D Michie; A C Wallace; M L Jones; J M Thornton
Journal:  Trends Biochem Sci       Date:  1997-12       Impact factor: 13.807

6.  Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis.

Authors:  H Sklenar; C Etchebest; R Lavery
Journal:  Proteins       Date:  1989

Review 7.  Conformation of polypeptides and proteins.

Authors:  G N Ramachandran; V Sasisekharan
Journal:  Adv Protein Chem       Date:  1968

8.  Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds.

Authors:  R C Wade; K J Clark; P J Goodford
Journal:  J Med Chem       Date:  1993-01-08       Impact factor: 7.446

9.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

10.  New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

Authors:  D N Boobbyer; P J Goodford; P M McWhinnie; R C Wade
Journal:  J Med Chem       Date:  1989-05       Impact factor: 7.446
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  305 in total

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5.  3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla.

Authors:  Bikash R Sahoo; Banikalyan Swain; Madhubanti Basu; Padmaja Panda; Nikhil K Maiti; Mrinal Samanta
Journal:  J Mol Model       Date:  2011-08-10       Impact factor: 1.810

6.  Small terminase couples viral DNA binding to genome-packaging ATPase activity.

Authors:  Ankoor Roy; Anshul Bhardwaj; Pinaki Datta; Gabriel C Lander; Gino Cingolani
Journal:  Structure       Date:  2012-07-05       Impact factor: 5.006

7.  Heterologous Expression and Functional Characterization of the Exogenously Acquired Aminoglycoside Resistance Methyltransferases RmtD, RmtD2, and RmtG.

Authors:  Laís L Corrêa; Marta A Witek; Natalia Zelinskaya; Renata C Picão; Graeme L Conn
Journal:  Antimicrob Agents Chemother       Date:  2015-11-09       Impact factor: 5.191

8.  Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.

Authors:  Eliza M Wiech; Hai-Ping Cheng; Shaneen M Singh
Journal:  Protein Sci       Date:  2014-12-26       Impact factor: 6.725

9.  Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins.

Authors:  Wei Ye; Dingjue Ji; Wei Wang; Ray Luo; Hai-Feng Chen
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10.  The Structural Basis for Cdc42-Induced Dimerization of IQGAPs.

Authors:  Louis LeCour; Vamsi K Boyapati; Jing Liu; Zhigang Li; David B Sacks; David K Worthylake
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