References

1. "ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions." Kumar MD, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, Uedaira H and Sarai A. Nuleic Acids Res. 2006; 34: D204-6.

2. "Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT)" P. Prabakaran, J. An, M. Gromiha, S. Selvaraj, H. Uedaira, H. Kono and A. Sarai. Bioinformatics. 2001; 17(11): 1027-34.

3. "Thermodynamic databases for proteins and protein-nucleic acid interactions" Sarai A, Gromiha MM, An J, Prabakaran P, Selvaraj S, Kono H, Oobatake M, Uedaira H. Biopolymers 2002; 61(2): 121-126.

Citation

If you use ProNIT as a tool in your published research work, please cite the above articles, including the URL.

Articles Cited ProNIT

• Analysis and Prediction

1. " Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling" Yoshida T, Nishimura T, Aida M, Pichierri F, Gromiha MM, Sarai A. Biopolymers. 2001-2002; 61(1): 84-95.

2. ""Protein-nucleic acid interactions. Web Alert" Philip E. Bourne, Judith Murray-Rust and Katrina L. Gill. Curr.Opin. Struct. Biol. 2002; 12: 9-10.

3. ""The evolution of structural databases." Oliviero Carugo and Sandor Pongor. Trends Biotechnol. 2002; 20(12): 498-501.

4. "Thermodynamics of specific protein-RNA interactions." Stolarski R. Acta Biochim Pol. 2003; 50(2): 297-318.

5. "Interaction of Protein Backbone with Nucleic Acid Bases" Alkorta ,I;Elguero ,J. J. Phys. Chem. B. 2003; 107(22): 5306-5310.

6. "Synthesis of stable-isotope (C-13 and N-15) labeled nucleotides and their applications" Kawashima E; Kamaike K. Mini-Reviews in Organic Chemistry 2004; 1(3): 309-332.

7. "Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential" Zhijie Liu, Fenglou Mao, Jun-tao Guo, BoYan, Peng Wang, Youxing Qu and Ying Xu. Nucleic Acids Res. 2005; Vol.33: 546-558.

8. "A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes" Zhang C,Liu S, Zhu QQ, Zhou YQ. J Med Chem. 2005; 48(7): 2325-35.

9. "Influence of DNA stiffness in protein-DNA recognition" Gromiha MM. J Biotechnol. 2005; 117(2): 137-45.

10. "Modeling DNA unzipping in the presence of bound proteins" Habib F, Bundschuh R. Phys Rev E Stat Nonlin Soft Matter Phys. 2005; 72(3 Pt 1):031906.

11. "Development of a plasmid display system using GAL4 DNA binding domain for the in vitro screening of functional proteins" Choi YS, Pack SP, Yoo YJ. Biotechnol Lett. 2005; 27(21): 1707-11.

12. "Protein-DNA binding specificity predictions with structural models" Alexandre V. Morozov, James J. Havranek, David Baker, and Eric D. Siggia. Nuleic Acids Res. 2005; 33: 5781-5798.

13. "Cataloging the relationships between proteins : a review of interaction databases." Rohl C, Price Y, Fischer TB, et al. MOLECULAR BIOTECHNOLOGY 2006; 34(1): 69-93.

14. "Point mutations in protein globular domains: Contributions from function, stability and misfolding." Sanchez IE, Tejero J, Gomez-Moreno C, et al. J Mol Biol. 2006; 363(2): 422-432.

15. "A backbone-based theory of protein folding." Rose GD, Fleming PJ, Banavar JR, et al. Proc Natl Acad Sci U S A. 2006; 103(45): 16623-33.

16. "Thermodynamics of neutral protein evolution." Bloom JD, Raval A, Wilke CO. Genetics. 2007; 175(1): 255-66.

17. "Is nonadditivity within double mutant cycles related to protein structure rigidity?." Istomin AY, Jacobs DJ, Gromiha MM, et al. BIOPHYSICAL JOURNAL. 2007; Suppl. S JAN : 217A-217A.

18. "Computational sidechain placement and protein mutagenesis with implicit solvent models." Lopes A, Alexandrov A, Bathelt C, et al. Proteins. 2007; 67(4): 853-67.

19. "Normal carbon acid referencing for protein amide hydrogen exchange." LeMaster DM, Anderson JS, Hernandez G. Magn Reson Chem. 2007; 45(7): 601-4.

20. "Genetic selection reveals the role of a buried, conserved polar residue." Johnson RJ, Lin SR, Raines RT. PROTEIN SCIENCE 2007; 16(8): 1609-1616.

21. "Protein thermal stability: The role of protein structure and aqueous environment ." Pechkova E, Sivozhelezov V, Nicolini C. Arch Biochem Biophys. 2007; 466(1): 40-8.

22. "Protein stability imposes limits on organism complexity and speed of molecular evolution ." Zeldovich KB, Chen PQ, Shakhnovich EI. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2007; 104(41): 16152-16157.

23. "Structural assessment of glycyl mutations in invariantly conserved motifs ." Prakash T, Sandhu KS, Singh NK, et al. Proteins. 2007; 69(3): 617-32.

24. "MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins." Bhardwaj N, Stahelin RV, Zhao GJ, et al. Bioinformatics. 2007; 23(22): 3110-2.

25. "Four-body scoring function for mutagenesis." Deutsch C, Krishnamoorthy B. Bioinformatics. 2007; 23(22): 3009-15.

26. "Free energy estimates of all-atom protein structures using Generalized Belief Propagation." Kamisetty H, Xing EP, Langmead CJ. J Comput Biol. 2008; 15(7): 755-66.

27. "New insight into long-range nonadditivity within protein double-mutant cycles." Istomin AY, Gromiha MM, Vorov OK, et al. Proteins. 2008; 70(3): 915-24.

28. "Prediction of recursive convex hull class assignments for protein residues." Stout M, Bacardit J, Hirst JD, et al. Bioinformatics. 2008; 24(7): 916-23.

29. "Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design ." Schmidt am Busch M, Lopes A, Amara N, et al. BMC BIOINFORMATICS 2008; Vol. 9: Article Number: 148.

30. " Integrating bioinformatics and computational biology: Perspectives and possibilities for in silico network reconstruction in molecular systems biology." Alves R, Vilaprinyo E, Sorribas A. CURRENT BIOINFORMATICS 2008; 3(2): 98-129.

31. "Understanding protein evolution: From protein physics to Darwinian selection." Zeldovich KB, Shakhnovich EI. Annu Rev Phys Chem. 2008; 59: 105-27.

32. "Understanding ensemble protein folding at atomic detail." Wallin S, Shakhnovich EI. JOURNAL OF PHYSICS-CONDENSED MATTER 2008; 20(28) Article Number: 283101.

33. "Structure and energetics of the hydrogen-bonded backbone in protein folding." Bolen DW, Rose GD. Annu Rev Biochem. 2008; 77: 339-62.

34. "Improvisation in evolution of genes and genomes: whose structure is it anyway?." Shakhnovich BE, Shakhnovich EI. Curr Opin Struct Biol. 2008; 18(3): 375-81.

35. "A three-state prediction of single point mutations on protein stability changes." Capriotti E, Fariselli P, Rossi I, et al. BMC BIOINFORMATICS 2008; Volume: 9 Article Number: S6 Supplement: Suppl. 2.

36. "Free energy estimates of all-atom protein structures using generalized belief propagation." Kamisetty H, Xing EP, Langmead CJ. J Comput Biol. 2008; 15(7): 755-66.

37. "Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins." Ahmad S, Keskin O, Sarai A, et al. Nucleic Acids Res. 2008; 36(18): 5922-32.

38. "Evaluation of the Stability of Folding Nucleus upon Mutation." Lonquety M, Lacroix Z, Chomilier J. PATTERN RECOGNITION IN BIOINFORMATICS, PROCEEDINGS Book Series: LECTURE NOTES IN BIOINFORMATICS Volume: 5265 Pages: 54-65 Published: 2008 .

39. "SPROUTS: a database for the evaluation of protein stability upon point mutation." Lonquety M, Lacroix Z, Papandreou N, et al. Nucleic Acids Res. 2009; 37(Database issue): D374-9.

40. "Dissection, residue conservation, and structural classification of protein-DNA interfaces." Biswas S, Guharoy M, Chakrabarti P. Proteins. 2009; 74(3): 643-54.

41. "Robust prediction of mutation-induced protein stability change by property encoding of amino acids." Kang SL, Chen G, Xiao GF. PROTEIN ENGINEERING DESIGN & SELECTION Volume: 22 Issue: 2 Pages: 75-83 Published: FEB 2009 .

42. "Genomic and structural aspects of protein evolution." Chothia C, Gough J. Biochem J. 2009; 419(1): 15-28.

43. "A survey of available tools and web servers for analysis of protein-protein interactions and interfaces." Tuncbag N, Kar G, Keskin O, et al. BRIEFINGS IN BIOINFORMATICS Volume: 10 Issue: 3 Pages: 217-232 Published: MAY 2009.

44. "Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin ." Bloom JD, Glassman MJ. PLOS COMPUTATIONAL BIOLOGY Volume: 5 Issue: 4 Article Number: e1000349 Published: APR 2009.

45. "Structural Stability of Amandin, a Major Allergen from Almond (Prunus dulcis), and Its Acidic and Basic Polypeptides." Albillos SM, Menhart N, Fu TJ. J Agric Food Chem. 2009; 57(11): 4698-705.

46. "Reliable prediction of protein thermostability change upon double mutation from amino acid sequence." Huang LT, Gromiha MM. Bioinformatics. 2009; 25(17): 2181-7.

47. "Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details." Potapov V, Cohen M, Schreiber G. Protein Eng Des Sel. 2009; 22(9): 553-60.

48. "BIPA: a database for protein-nucleic acid interaction in 3D structures." Lee S, Blundell TL. Bioinformatics. 2009; 25(12): 1559-60.

• Books

1. Jarl E.S. Wikberg, Maris Lapainsh and Peteris Prusis.
   Proteochemometrics.
   In "Chemogenomics in Drug Discover A Medicinal Chemistry Perspective Methods and Principles in Medicinal Chemistry" Kubinyi, Hugo/Mueller, Gerhard (eds.), Wiley-VCH, Weinheim, 2004
   

2. A. Sarai, P Prabakaran and H Uedaira.
   "Thermodynamic database for Protein-Nucleic Acid Interaction (ProNIT)" in Comprehensive Handbook of Calorimetry and Thermal Analysis. John Wiley & Sons, Ltd. (2004) [ISBN: 0-470-85152-X]
   

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