References

If you need to cite STING, JPD, STING REPORT and other STING components, please do so by referring to corresponding paper from the list bellow:

 

1: R.C. Melo, C. Ribeiro, C.S. Murray, C.J.M. Veloso, C.H.. da Silveira, Goran Neshich, W. Meira Jr, R.L. Carceroni and M.M. Santoro.

 

"Finding protein-protein interactions patterns by contact-maps matching: BPTI-Serine Protease complexes as a case study."
Genet. Mol. Res. 6(3) 2007.

 

2: Walter Rocchia and Goran Neshich.
 

"Electrostatic Potential Calculation for biomolecules - creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures."
Genet. Mol. Res. 6(3) 2007.

 

3: Stanley R. M. Oliveira, Gustavo V. Almeida, Kassyus R. R. Souza, Diego N. Rodrigues, Paula R. Kuser-Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José G. Jardine and Goran Neshich.
 

"STING_RDB: A relational database of structural parameters for protein analysis with support for Data Warehousing and Data Mining."
Genet. Mol. Res. 6(3) 2007.

 

4: Yamagishi ME, Martins NF, Neshich G, Cai W, Shao X, Beautrait A, Maigret B.
 

"A fast surface matching procedure for protein-ligand docking."
J Mol Model (Online). 2006 May 4;
PMID: 16673083

 

5: HIGA, Roberto; KUSER, Paula; MICHEL, Yamagishi; MANCINI, Adauto; NESHICH, Goran.
 

"Building Multiple Sequence Alignments with a flavour of HSSP alignments."
Genet. Mol. Res. 5 (1) 2006.

 

6: Luiz C. Borro, Stanley R.M. Oliveira, Michel E.B. Yamagishi, Adaulto L. Mancini, José G. Jardine, Ivan Mazoni, Edgard H. dos Santos, Roberto H. Higa, Paula R. Kuser and Goran Neshich.
 

"Predicting enzyme class from protein structure using Bayesian classification."
Genet. Mol. Res. 5 (1) 2006.

 

7: Renato Fileto, Paula R. Kuser, Michel E. B. Yamagishi, André A. Ribeiro, Thiago G. Quinalia, Eduardo H. Franco, Adauto L. Mancini, Roberto H. Higa, Stanley R. M. Oliveira, Edgard H. Santos, Fabio D. Vieira, Ivan Mazoni, Sergio A. B. Cruz, Goran Neshich.
 

"PDB-metrics: a web tool for exploring the PDB contents."
Genet. Mol. Res. 5 (2) 2006.

 

8: Goran Neshich, Ivan Mazoni, Stanley R. M. Oliveira, Michel E. B. Yamagishi, Paula R. Kuser-Falcão, Luiz C. Borro, Douglas U. Morita, Kassyus R. R. Souza, Gustavo V. Almeida, Diego N. Rodrigues, José G. Jardine, Roberto C. Togawa, Adauto L. Mancini, Roberto H. Higa, Sérgio A. B. Cruz, Fábio D. Vieira, Edgard H. dos Santos, Raquel C. de Melo and Marcelo M. Santoro.
 

"The Star STING server: A multiplatform environment for protein structure analysis."
Genet. Mol. Res. 5 (4) 2006.

 

9: Neshich G, Borro LC, Higa RH, Kuser PR, Yamagishi 15980473ME, Franco EH, Krauchenco JN, Fileto R, Ribeiro AA, Bezerra GB, Velludo TM, Jimenez TS, Furukawa N, Teshima H, Kitajima K, Bava A, Sarai A, Togawa RC, Mancini AL.
 

"Diamond STING: an expanded functionality for the STING suite of programs allowing the comprehensive sequence/structure/function/stability analysis with added capability for handling local files."
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W29-35.
PMID: 15980473

 

10: Neshich G, Mancini AL, Yamagishi ME, Kuser PR, Fileto R, Pinto IP, Palandrani JF, Krauchenco JN, Baudet C, Montagner AJ, Higa RH.
 

"STING Report: collection of graphic and tabular sequence structure and function descriptors for an individual amino acid of PDB structures."
Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D269-74.
PMID: 15608194

 

11: Higa RH, Togawa RC, Montagner AJ, Palandrani JC, Okimoto IK, Kuser PR, Yamagishi ME, Mancini AL, Neshich G.
 

"STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes."
BMC Bioinformatics. 2004 Aug 09;5(1):107.
PMID: 15301693

 

12: Neshich G, Rocchia W, Mancini AL, Yamagishi ME, Kuser PR, Fileto R, Baudet C, Pinto IP, Montagner AJ, Palandrani JF, Krauchenco JN, Torres RC, Souza S, Togawa RC, Higa RH.
 

"JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure."
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W595-601.
PMID: 15215458

 

13: Mancini AL, Higa RH, Oliveira A, Dominiquini F, Kuser PR, Yamagishi ME, Togawa RC, Neshich G.
 

"STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces."
Bioinformatics. 2004 Sep 1;20(13):2145-7. Epub 2004 Apr 08.
PMID: 15073001

 

14: Higa RH, Montagner AJ, Togawa RC, Kuser PR, Yamagishi ME, Mancini AL, Pappas G Jr, Miura RT, Horita LG, Neshich G.
 

"ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure."
Bioinformatics. 2004 Aug 12;20(12):1983-5. Epub 2004 Mar 25.
PMID: 15044236

 

15: Higa RH, Oliveira AG, Horita LG, Miura RT, Inoue MK, Kuser PR, Mancini AL, Yamagishi ME, Togawa RC, Neshich G.
 

"Defining 3D residue environment in protein structures using SCORPION and FORMIGA."
Bioinformatics. 2004 Aug 12;20(12):1989-91. Epub 2004 Mar 25.
PMID: 15044232

 

16: Neshich G, Togawa RC, Mancini AL, Kuser PR, Yamagishi ME, Pappas G Jr, Torres WV, Fonseca e Campos T, Ferreira LL, Luna FM, Oliveira AG, Miura RT, Inoue MK, Horita LG, de Souza DF, Dominiquini F, Alvaro A, Lima CS, Ogawa FO, Gomes GB, Palandrani JF, dos Santos GF, de Freitas EM, Mattiuz AR, Costa IC, de Almeida CL, Souza S, Baudet C, Higa RH.
 

"STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence."
Nucleic Acids Res. 2003 Jul 1;31(13):3386-92.
PMID: 12824333

 

17: G. Neshich, Roberto Togawa and Barry Honig.
 

"Sequence To and withIN Graphics PDB Viewer (STING -PDB viewer)."
PDB Quarterly NewsLetter, July 1998, page 6

 

18: G. Neshich, Roberto Togawa, Jaime Prilusky, Joel Suussman and Barry Honig.
 

"Searching for the Right PDB File with the 3DB Browser and Displaying Structure and Sequence Data with STING."
PDB Quarterly NewsLetter, July 1998, page 7

 

Sting Applications

 

1: Da Silva M.C.M., Grossi de Sá M.F., Chrispeels M.J., Togawa R.C. and G. Neshich.

 

"Analysis of Structural and Physico-chemical Parameters Involved in the Specificity of Binding between Alpha-Amylases and their Inhibitors."
Protein Engineering, Vol. 13, No. 3, 167-177, March 2000.

 

2: Caldas, C.A., Coelho, V.P.C.V., Rigden, D., G. Neshich, Moro, A.M. and Brigido, M.
 

"Design and synthesis of germline-based hemi-humanized single chain Fv against the CD18 surface antigen."
Protein Engineering Vol. 13, No.5, 353-360, May 2000

 

3: Fernandez J. H., Hayashi M.A.F., Camargo A.C.M. 1 and G. Neshich.
 

"Structural basis of the lisinopril binding specificity in N and C domains of human somatic ACE."
BBRC: Biochemical and Biophysical Research Communications 308 (2003)219-226

 

4: Marcellino LH, Neshich G, Neto AF, Gander ES.
 

"An opaque-2-like transcription factor from pearl millet."
Protein Pept Lett. 2004 Aug;11(4):345-52.

 

5: SILVA, Maria Cristina Mattar da; MELLO, Luciane V de; COUTINHO, Marise Ventura; RIGDEN, Daniel John; Goran Neshich; CHRISPEELS, Maarten John; GROSSI DE SA, Maria Fatima.
 

"Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases."
Pesquisa Agropecuária Brasileira, Brazil, v. 39, n. 3, p. 201-208, 2004

 

6: HERNANDEZ, Jorge Fernandez; NESHICH, Goran; ACM, Camargo.
 

"Using bradykinim potentiating peptide (BPP) structures to develop new antihipertensive drugs."
Genet. Mol. Res, Riberao Preto, v. 3, n. 4, p. 554-563, 2005.

 

7: M.C. Simões; D. Bahia; A.Z. Neto; K. Torres; F. Artiguenave; G. Neshich; P.R. Kuser, G.C. Oliveira.
 

"Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni."
Molecular and Biochemical Parasitology, in press, 2007.

 

8: Jorge H. Fernandez, Marcia O. Mello, Leticia Galgaro, Aparecida S. Tanaka, Marcio C. Silva-Filho, Goran Neshich.
 

"Proteinase inhibition using small Bowman-Birk type structures."
Genet. Mol. Res. 6(1) 2007

 

9: R.C. Melo, C. Ribeiro, C.S. Murray, C.J.M. Veloso, C.H.. da Silveira, Goran Neshich, W. Meira Jr, R.L. Carceroni and M.M. Santoro.
 

"Finding protein-protein interactions patterns by contact-maps matching: BPTI-Serine Protease complexes as a case study."
Genet. Mol. Res. 6(1) 2007

 

10: R. C. Togawa, C. Ribeiro, I. Mazoni, T. Pelligrinelli, and NESHICH, Goran
 

" The Table of Interface Forming Residues as the Specificity Indicator for Serine Proteases Bound to Different Inhibitors "
Accepted: BIOCOMP 08, 2008.

 

11: Cristina Ribeiro, Roberto C Togawa, Izabella AP Neshich, Ivan Mazoni, Adauto L Mancini, Raquel C de Melo Minardi, Carlos H da Silveira, José G Jardine, Marcelo M Santoro, Goran Neshich
 

"Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors"
BMC Structural Biology 2010, 10:36

 

Also:

  • Goran Neshich, Roberto Togawa, Wellington Vilella and Barry Honig

    "STING (Sequence To and withIN     Graphics) PDB_Viewer"

    Protein Data Bank Quarterly Newsletter 84, July 1998.

    • Acknowledgements:
    We would like to thank to Prof. Bernard Maigret for valuable input and ideas that he shared with us, specifically for Ca-Ca and Cb-Cb contacts and aromatic stacking type of contacts.
    We would like to thank Sridhara Sridharan for providing SURFV program (used in IFR_contacts and FORMIGA for calculation of solvent accessible area).