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Total number of citations : 197

References

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

  2. " "ProTherm, version 4.0: Thermodynamic Database for Proteins and Mutants"
    K. Abdulla Bava, M. Michael Gromiha, H. Uedaira, Koji Kitajima and A. Sarai (2004).
    Nucleic Acids Res. 32, D120-D121, Database issue

  3. " "ProTherm,Thermodynamic Database for Proteins and Mutants:Developments in Version 3.0"
    M. Michael Gromiha, H. Uedaira, J. An, S. Selvaraj, P. Prabakaran and A. Sarai (2002).
    Nucleic Acids Res. 30, 301-302

  4. " "Thermodynamic Databases for Proteins and Protein-Nucleic Acid Interactions"
    A. Sarai, M.M. Gromiha, J. An, P. Prabakaran, S. Selvaraj, H. kono, M. Oobatake and H. Uedaira (2002).
    Biopolymers 61, 121-126

  5. " "ProTherm, version 2.0: thermodynamic Database for Proteins and Mutants"
    M. Michael Gromiha, J. An, H. Kono, M. Oobatake, H. Uedaira, P. Prabakaran and A. Sarai (2000)
    Nucleic Acids Res. 28,283-285.

  6. " "ProTherm: Thermodynamic Database for Proteins and Mutants"
    M. Michael Gromiha, J. An, H. Kono, M. Oobatake, H. Uedaira and A. Sarai (1999)
    Nucleic Acids Res. 27, 286-288.


Citing ProTherm

If you use ProTherm as a tool in your published research work, please cite the latest article, including the URL.

Articles Cited ProTherm

    1. Chen JM, Lu ZQ, Sakon J, Stites WE
      Increasing the thermostability of staphylococcal nuclease: Implications for the origin of protein thermostability
      J MOL BIOL 303 (2): 125-130 OCT 20 2000

    2. Beadle BM, Shoichet BK.
      Structural Bases of Stability-function Tradeoffs in Enzymes.
      J Mol Biol 2002 Aug 9;321(2):285-296

    3. Krittanai C, Bourchookarn A, Pathaichindachote W, Panyim S
      Mutation of the hydrophobic residue on helix alpha 5 of the Bacillus thuringiensis Cry4B affects structural stability.
      PROTEIN PEPTIDE LETT 10(4):361-368 AUG 2003

    4. Schoeffler AJ, Joubert AM, Peng F,Khan F, Liu CC, LiCata VJ.
      Extreme free energy of stabilization of Taq DNA polymerase.
      Proteins. 2004 Mar 1;54(4):616-21.

    5. Gromiha MM, Pujadas G,Magyar C, Selvaraj S, Simon I.
      Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation.
      Proteins. 2004 May 1;55(2):316-29.

    6. Sheldon Park, Hidetoshi Kono, Wei Wang, Eric T. Boder and Jeffery G. Saven
      Progress in the development and application of computational methods for probabilistic protein design.
      Computers & Chemical Engineering, Volume 29, Issue 3, 15 February 2005, Pages 407-421

    7. Jayachithra K, Kumar TK, Lu TJ, Yu C, Chin DH.
      Cold instability of aponeocarzinostatin and its stabilization by labile chromophore.
      Biophys J. 2005 Jun;88(6)4252-61. Epub 2005 Apr 8.

    8. Lemaster DM, Hernandez G.
      Additivity in Both Thermodynamic Stability and Thermal Transition Temperature for Rubredoxin Chimeras via Hybrid Native Partitioning.
      Structure (Camb). 2005 Aug;13(8):1153-63

    9. Bastolla U, Demetrius L
      Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds
      PROTEIN ENGINEERING DESIGN & SELECTION 18(9):405-415 SEP 2005

    10. Macao B, Johansson D GA, Hansson GC, et al.
      Autoproteolysis coupled to protein folding in the SEA domain of the membrane-bound MUC1 mucion
      NATURE STRUCTURAL & MOLECULAR BIOLOGY 13(1): 71-76 JAN 2006

    11. Trevino SR, Gokulan K, Newsom S, et al.
      Asp 79 makes a large, unfavorable contribution to the stability of RNase Sa
      JOURNAL OF MOLECULAR BIOLOGY 354 (4): 967-978 DEC 9 2005

    12. Wu Lc, Horng JT, Huang SL, et al.
      Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures
      JOURNAL OF COMPUTATIONAL CHEMISTRY 27 (6): 798-808 APR 30 2006

    13. Wu LC, Horng JT, Huang SL, Huang HD, Liu BJ
      Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures.
      J Comput Chem. 2006 Apr 30;27(6):798-808

    14. Bloom JD, Labthavikul ST, Otey CR, et al.
      Protein stability promotes evolvability
      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (15) : 5869-5874 APR 11 2006

    15. Razvi A, Scholtz JM
      Lessons in stability from thermophilic proteins
      PROTEIN SCIENCE 15 (7) : 1569-1578 JUL 2006

    16. Tanaka T, Sawano M, Ogasahara K, et al.
      Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 degrees C
      FEBS LETTERS 580 (17) : 4224-4230 JUL 24 2006

    17. Rose GD, Fleming PJ, Banavar JR, et al.
      A backbone-based theory of protein folding
      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (45): 16623-16633 NOV 7 2006

    18. Bloom JD, Raval A, Wilke CO.
      Thermodynamics of neutral protein evolution
      GENETICS 175 (1): 255-266 JAN 2007

    19. LeMaster DM, Hernandez G.
      Residue cluster additivity of thermodynamic stability in the hydrophobic core of mesophile vs. hyperthermophile rubredoxins
      BIOPHYSICAL CHEMISTRY 125 (2-3): 483-489 FEB 2007

    20. Bloom JD, Lu Z, Chen D, et al.
      Evolution favors protein mutational robustness in sufficiently large populations
      BMC BIOLOGY 5: Art. No. 29 JUL 17 2007

  • General
    1. Kresten Lindorff-Larsen, Emanuele Paci, Luis Serrano, Christopher M. Dobson and Michele Vendruscolo
      Calculation of Mutational Free Energy Changes in Transition States for Protein Folding.
      Biophys. J. 2003 85(2): p. 1207-1214

    2. Rossane C. DeLapp,Eugene J. LeBoeuf, and Katherine D. Bell
      Thermodynamic properties of several soil- and sediment-derived natural organic materials
      Chemosphere 2004 54(4): 527-539

    3. Triantafillidou D,Persidou E,Lazarou D, et al.
      Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid \substitution
      BIOL CHEM 385 (1):31-39 JAN 2004

    4. Monsellier E,Bedouelle H
      Quantitative measurement of protein stability from unfolding equilibria monitored with the fluorescence maximum wavelength
      PROTEIN ENGINEERING DESIGN & SELECETION 18(9):445-456 SEP 2005

    5. Yue P, Li Z, Moult J.
      Loss of protein structure stability as a major causative factor in monogenic disease.
      J Mol Biol. 2005 Oct 21;353(2):459-73.

    6. Choi YS, Joo H, Yoo YJ.
      In vitro selection of high affinity DNA-binding protein based on plasmid display technology
      JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY 15 (5):1022-1027 OCT 2005

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

    8. Greaves RB, Warwicker J
      Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles
      BMC STRUCTURAL BIOLOGY 7: Art. No. 18 MAR 29 2007

    9. Lopes A, Alexandrov A, Bathelt C, et al.
      Computational sidechain placement and protein mutagenesis with implicit solvent models
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 67 (4): 853-867 JUN 2007

    10. LeMaster DM, Anderson JS, Hernandez G
      Normal carbon acid referencing for protein amide hydrogen exchange
      MAGNETIC RESONANCE IN CHEMISTRY 45 (7): 601-604 JUL 2007

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

    12. Matsui I, Harata K
      Implication for buried polar contacts and ion pairs in hyperthermostalble enzymes
      FEBS JOURNAL 274 (16): 4012-4022 AUG 2007

    13. Dehouck Y, Folch B, Rooman M
      Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity
      PROTEIN ENGINEERING DESIGN & SELECTION, 21 (4): 275-278, Apr 2008

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

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

    16. Shakhnovich BE, Shakhnovich EI
      Improvisation in evolution of genes and genomes: whose structure is it anyway?
      CURRENT OPINION IN STRUCTURAL BIOLOGY, 18 (3) : 375-381, Jun 2008

    17. Shckorbatov Y, Berezhnoy A
      Similarities in protein amino acid composition in connection with principles of protein evolution
      CENTRAL EUROPEAN JOURNAL OF BIOLOGY, 3 (2): 205-209, Jun 2008

    18. Lonquety M, Lacroix Z, Chomilier J
      Evaluation of the Stability of Folding Nucleus upon Mutation Conference Information: 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, OCT 15-17, 2008 Melbourne, AUSTRALIA
      PATTERN RECOGNITION IN BIOINFORMATICS, PROCEEDINGS Book Series: LECTURE NOTES IN BIOINFORMATICS, 5265: 54-65, 2008

    19. Tokuriki N, Oldfield CJ, Uversky VN, et al.
      Do viral proteins possess unique biophysical features?
      TRENDS IN BIOCHEMICAL SCIENCES, 34 (2): 53-59, Feb 2009

    20. Chothia C, Gough J
      Genomic and structural aspects of protein evolution
      BIOCHEMICAL JOURNAL, 419: 15-28 Part 1, Apr 2009

    21. Sangcharoen A, Tepanant W, Kidsanguan S, et al.
      Investigation of the unfolding pathway of Bacillus thuringiensis Cyt2Aa2 toxin reveals an unfolding intermediate
      JOURNAL OF BIOTECHNOLOGY, 141 (3-4): 137-141, May 2009

    22. Albillos SM, Menhart N, Fu TJ
      Structural Stability of Amandin, a Major Allergen from Almond (Prunus dulcis), and Its Acidic and Basic Polypeptides
      JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 57 (11): 4698-4705, Jun 2009

    23. Sawano M, Yamamoto H, Ogasahara K, et al.
      Thermodynamic basis for the stabilities of three CutA1s from Pyrococcus horikoshii, Thermus thermophilus, and Oryza sativa, with unusually high denaturation temperatures
      BIOCHEMISTRY, 47 ( 2): 721-730, Jan 2008

    24. Bloom JD, Glassman MJ
      Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
      PLOS COMPUTATIONAL BIOLOGY, 5 (4) Art. No: e1000349, Apr 2009

    25. Tartaglia GG, Pechmann S, Dobson CM, et al.
      A Relationship between mRNA Expression Levels and Protein Solubility in E. coli
      JOURNAL OF MOLECULAR BIOLOGY, 388 (2): 381-389, May 2009

    26. Albillos SM, Menhart N, Fu TJ.
      Structural stability of Amandin, a major allergen from almond (Prunus dulcis), and its acidic and basic polypeptides.
      J Agric Food Chem. 2009 Jun 10;57(11):4698-705. PMID: 19374443

    27. PC)rez AG, Angarica VE, Collado-Vides J, Vasconcelos AT.
      From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters.
      BMC Mol Biol. 2009 Sep 22;10:92. PMID: 19772633

    28. Chen P, Shakhnovich EI.
      Lethal mutagenesis in viruses and bacteria.
      Genetics. 2009 Oct;183(2):639-50. Epub 2009 Jul 20. PMID: 19620390

    29. Lee S, Brown A, Pitt WR, Higueruelo AP, Gong S, Bickerton GR, Schreyer A, Tanramluk D, Baylay A, Blundell TL.
      Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics.
      Mol Biosyst. 2009 Dec;5(12):1456-72. Epub 2009 Aug 6. PMID: 19763326

    30. Ruiz-PeC1a M, Oropesa-NuC1ez R, Pons T, Louro SR, PC)rez-Gramatges A.
      Physico-chemical studies of molecular interactions between non-ionic surfactants and bovine serum albumin.
      Colloids Surf B Biointerfaces. 2010 Jan 1;75(1):282-9. Epub 2009 Sep 4. PMID: 19782541

    31. Folch B, Dehouck Y, Rooman M.
      Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials.
      Biophys J. 2010 Feb 17;98(4):667-77. PMID: 20159163

    32. Rajasekaran R, Sethumadhavan R.
      In silico identification of significant detrimental missense mutations of EGFR and their effect with 4-anilinoquinazoline-based drugs.
      Appl Biochem Biotechnol. 2010 Mar;160(6):1723-33. Epub 2009 May 20. PMID: 19455431

    33. Roman EA, Arguello JM, GonzC!lez Flecha FL.
      Reversible unfolding of a thermophilic membrane protein in phospholipid/detergent mixed micelles.
      J Mol Biol. 2010 Mar 26;397(2):550-9. Epub 2010 Jan 28. PMID: 20114054

    34. Chen P, Shakhnovich EI.
      Thermal adaptation of viruses and bacteria.
      Biophys J. 2010 Apr 7;98(7):1109-18. PMID: 20371310

    35. FernC!ndez A, Berry RS.
      Golden rule for buttressing vulnerable soluble proteins.
      J Proteome Res. 2010 May 7;9(5):2643-8. PMID: 20364868

    36. Seeliger D, de Groot BL.
      Protein thermostability calculations using alchemical free energy simulations.
      Biophys J. 2010 May 19;98(10):2309-16. PMID: 20483340

    37. Tartaglia GG, Dobson CM, Hartl FU, Vendruscolo M.
      Physicochemical determinants of chaperone requirements.
      J Mol Biol. 2010 Jul 16;400(3):579-88. Epub 2010 Apr 21. PMID: 20416322

    38. Mehta KR, Chan YM, Lee MX, Yang CY, Voloshchuk N, Montclare JK.
      Mutagenesis of tGCN5 core region reveals two critical surface residues F90 and R140.c
      Biochem Biophys Res Commun. 2010 Sep 24;400(3):363-8. Epub 2010 Aug 21. PMID: 20732305

    39. Plata G, Gottesman ME, Vitkup D.
      The rate of the molecular clock and the cost of gratuitous protein synthesis.
      Genome Biol. 2010;11(9):R98. Epub 2010 Sep 29. PMID: 20920270

    40. Huang LT, Lai LF, Gromiha MM.
      Human-readable rule generator for integrating amino scid sequence information and stability of mutant proteins.
      IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):681-7. PMID: 21030735

  • Reviews
  • Books
    1. Pfeil, W.
      Protein stability and folding, Supplement 1: A collection of thermodynamic data
      Springer-Verlag, New York, 2001
    2. Ooi. T and Shimizu, S.
      Molecular life of proteins: Folding and stability.
      In "Recent Research Developments in Protein Folding, Stability and Design" (Ed. M. Michael Gromiha and S. Selvaraj), pp 243-264,Research Signpost,
      Trivandrum, India (2002).
    3. Krebs, WG and Bourne, PE.
      The Protein Mutant Resource: Visual and Statistical Analysis of Mutations with Implications for Homology Modeling.
      In "Currents in Computational Molecular Biology 2004" (Eds. A. Gramada and PE. Bourne) pp 48-49 (2004).

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