Wenxiang: a web-server for drawing wenxiang diagrams

The wenxiang diagram was proposed to represent α-helices in a 2D (two dimensional) space (Chou, K.C., Zhang, C.T., Maggiora, G.M. Proteins: Struct., Funct., Genet., 1997, 28, 99-108). It has the capacity to provide more information in a 2D plane about each of the constituent amino acid residues in an α-helix, and is particularly useful for studying and analyzing amphiphilic helices. To meet the increasing requests for getting the program of generating wenxiang diagrams, a user-friendly web-server called “Wenxiang” has been established. It is accessible to the public at the web-site http://www.jci-bioinfo.cn/wenxiang2 or http://icpr.jci.edu.cn/bioinfo/wenxiang2. Furthermore, for the convenience of users, here we provide a step-to-step guide for how to use the Wenxiang web-server to generate the desired wenxiang diagrams.

[1]  M. Schiffer,et al.  Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. , 1967, Biophysical journal.

[2]  S. Forsén,et al.  Graphical rules for enzyme-catalysed rate laws. , 1980, The Biochemical journal.

[3]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[4]  K. Chou,et al.  Identification of low-frequency modes in protein molecules. , 1983, The Biochemical journal.

[5]  G. Zhou,et al.  An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. , 1984, The Biochemical journal.

[6]  Kuo-Chen Chou,et al.  Energetic approach to the packing of α-helices. II: General treatment of nonequivalent and nonregular helices , 1984 .

[7]  K. Chou,et al.  Low-frequency collective motion in biomacromolecules and its biological functions. , 1988, Biophysical chemistry.

[8]  K. Chou,et al.  Low-frequency resonance and cooperativity of hemoglobin. , 1989, Trends in biochemical sciences.

[9]  K. Chou,et al.  Graphic rules in steady and non-steady state enzyme kinetics. , 1989, The Journal of biological chemistry.

[10]  K. Chou Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady-state systems. , 2020, Biophysical chemistry.

[11]  P Martel,et al.  Biophysical aspects of neutron scattering from vibrational modes of proteins. , 1992, Progress in biophysics and molecular biology.

[12]  J. Chou,et al.  Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204E. , 1993, Biochemistry.

[13]  L. Resnick,et al.  The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. , 1993, The Journal of biological chemistry.

[14]  J. Chou,et al.  Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. , 1993, The Journal of biological chemistry.

[15]  K C Chou,et al.  Kinetics of processive nucleic acid polymerases and nucleases. , 1994, Analytical biochemistry.

[16]  G M Maggiora,et al.  Disposition of amphiphilic helices in heteropolar environments , 1997, Proteins.

[17]  K. Chou,et al.  Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image. , 2008, Journal of theoretical biology.

[18]  J. Andraos Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws — New methods based on directed graphs , 2008 .

[19]  Kuo-Chen Chou,et al.  GPCR‐CA: A cellular automaton image approach for predicting G‐protein–coupled receptor functional classes , 2009, J. Comput. Chem..

[20]  Jiangning Song,et al.  Prediction of protein folding rates from primary sequence by fusing multiple sequential features , 2009 .

[21]  K. Chou,et al.  2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. , 2010, Journal of theoretical biology.

[22]  K. Chou Graphic rule for drug metabolism systems. , 2010, Current drug metabolism.

[23]  Guo-Ping Zhou The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein–protein interaction mechanism , 2011, Journal of Theoretical Biology.

[24]  Guo-Ping Zhou,et al.  The structural determinations of the leucine zipper coiled-coil domains of the cGMP-dependent protein kinase Iα and its interaction with the myosin binding subunit of the myosin light chains phosphase. , 2011, Protein and peptide letters.