Literature DB >> 19805347

Fast screening of protein surfaces using geometric invariant fingerprints.

Shuangye Yin1, Elizabeth A Proctor, Alexey A Lugovskoy, Nikolay V Dokholyan.   

Abstract

We develop a rapid and efficient method for the comparison of protein local surface similarities using geometric invariants (fingerprints). By combining fast fingerprint comparison with explicit alignment, we successfully screen the entire Protein Data Bank for proteins that possess local surface similarities. Our method is independent of sequence and fold similarities, and has potential application to protein structure annotation and protein-protein interface design.

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Year:  2009        PMID： 19805347      PMCID： PMC2757799          DOI： 10.1073/pnas.0906146106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  23 in total

1.  Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

Authors:  Richard J Morris; Rafael J Najmanovich; Abdullah Kahraman; Janet M Thornton
Journal:  Bioinformatics       Date:  2005-02-22       Impact factor: 6.937

2.  A fourier fingerprint-based method for protein surface representation.

Authors:  Martin J Bayley; Eleanor J Gardiner; Peter Willett; Peter J Artymiuk
Journal:  J Chem Inf Model       Date:  2005 May-Jun       Impact factor: 4.956

3.  Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.

Authors:  Nicola D Gold; Richard M Jackson
Journal:  J Mol Biol       Date:  2005-12-01       Impact factor: 5.469

4.  Fast protein tertiary structure retrieval based on global surface shape similarity.

Authors:  Lee Sael; Bin Li; David La; Yi Fang; Karthik Ramani; Raif Rustamov; Daisuke Kihara
Journal:  Proteins       Date:  2008-09

5.  TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.

Authors:  A C Wallace; N Borkakoti; J M Thornton
Journal:  Protein Sci       Date:  1997-11       Impact factor: 6.725

6.  Reduced surface: an efficient way to compute molecular surfaces.

Authors:  M F Sanner; A J Olson; J C Spehner
Journal:  Biopolymers       Date:  1996-03       Impact factor: 2.505

7.  Protein structure comparison by alignment of distance matrices.

Authors:  L Holm; C Sander
Journal:  J Mol Biol       Date:  1993-09-05       Impact factor: 5.469

8.  A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures.

Authors:  P J Artymiuk; A R Poirrette; H M Grindley; D W Rice; P Willett
Journal:  J Mol Biol       Date:  1994-10-21       Impact factor: 5.469

Review 9.  Catalytic triads and their relatives.

Authors:  G Dodson; A Wlodawer
Journal:  Trends Biochem Sci       Date:  1998-09       Impact factor: 13.807

10.  TM-align: a protein structure alignment algorithm based on the TM-score.

Authors:  Yang Zhang; Jeffrey Skolnick
Journal:  Nucleic Acids Res       Date:  2005-04-22       Impact factor: 16.971
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  16 in total

1.  Fingerprint-based structure retrieval using electron density.

Authors:  Shuangye Yin; Nikolay V Dokholyan
Journal:  Proteins       Date:  2011-01-03

2.  Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction.

Authors:  Tianyi Qiu; Han Xiao; Qingchen Zhang; Jingxuan Qiu; Yiyan Yang; Dingfeng Wu; Zhiwei Cao; Ruixin Zhu
Journal:  PLoS One       Date:  2015-04-22       Impact factor: 3.240

3.  Rigid substructure search.

Authors:  David Shirvanyants; Anastassia N Alexandrova; Nikolay V Dokholyan
Journal:  Bioinformatics       Date:  2011-04-01       Impact factor: 6.937

Review 4.  Pocket-based drug design: exploring pocket space.

Authors:  Xiliang Zheng; Linfeng Gan; Erkang Wang; Jin Wang
Journal:  AAPS J       Date:  2012-11-22       Impact factor: 4.009

5.  Speeding up the drug discovery process: structural similarity searches using molecular surfaces.

Authors:  Dimitrios Vlachakis; Georgia Tsiliki; Dimosthenis Tsagkrasoulis; Carla Sofia Carvalho; Vasileios Megalooikonomou; Sofia Kossida
Journal:  EMBnet J       Date:  2012

6.  Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator.

Authors:  Chi Wang; Andrei A Aleksandrov; Zhengrong Yang; Farhad Forouhar; Elizabeth A Proctor; Pradeep Kota; Jianli An; Anna Kaplan; Netaly Khazanov; Grégory Boël; Brent R Stockwell; Hanoch Senderowitz; Nikolay V Dokholyan; John R Riordan; Christie G Brouillette; John F Hunt
Journal:  J Biol Chem       Date:  2018-06-14       Impact factor: 5.157

7.  Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way.

Authors:  Juliette Martin
Journal:  PLoS Comput Biol       Date:  2010-06-17       Impact factor: 4.475

Review 8.  On the binding affinity of macromolecular interactions: daring to ask why proteins interact.

Authors:  Panagiotis L Kastritis; Alexandre M J J Bonvin
Journal:  J R Soc Interface       Date:  2012-12-12       Impact factor: 4.118

9.  PoSSuM: a database of similar protein-ligand binding and putative pockets.

Authors:  Jun-Ichi Ito; Yasuo Tabei; Kana Shimizu; Koji Tsuda; Kentaro Tomii
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

10.  Protein surface characterization using an invariant descriptor.

Authors:  Zainab Abu Deeb; Donald A Adjeroh; Bing-Hua Jiang
Journal:  Int J Biomed Imaging       Date:  2011-11-22
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