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

• Analysis and Prediction

  1. Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A.
     Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations.
     Protein Eng. 1999 Jul;12(7):549-55.

  2. Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A.
     Relationship between amino acid properties and protein stability: buried mutations.
     J Protein Chem. 1999 Jul;18(5):565-78.

  3. Muthusamy R, Gromiha MM, Ponnuswamy PK
     On the thermal unfolding character of globular proteins
     JOURNAL OF PROTEIN CHEMISTRY 19(1):1-8 JAN 2000

  4. Areshev AG, Mamaeva OK, Andreeva NS, et al.
     Structure of glutamate decarboxylase and related PLP-enzymes: Computer-graphical studies
     JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 18 (1): 127-136 AUG 2000

  5. Ooi T
     Thermal stability of a protein predicted from its three dimensional structure
     P JPN ACAD B-PHYS 76 (7): 97-102 SEP 2000

  6. Gromiha MM, Thangakani AM
     Role of medium- and long-range interactions to the stability of the mutants of T4 lysozyme
     PREPARATIVE BIOCHEMISTRY & BIOTECHNOLOGY 31 (3): 217-227 2001

  7. Gromiha MM
     Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins
     BIOPHYSICAL CHEMISTRY 91 (1): 71-77 JUN 15 2001

  8. Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A.
     Importance of surrounding residues for protein stability of partially buried mutations.
     J Biomol Struct Dyn. 2000 Oct;18(2):281-95.

  9. Ragone R.
     Hydrogen-bonding classes in proteins and their contribution to the unfolding reaction.
     Protein Sci. 2001 Oct;10(10)2075-82

  10. Kumar S, Tsai C-J, Nussinov R.
      Thermodynamic Differences among Homologous Thermophilic and MesophilicProteins.
      Biochemistry, 40 (47), 14152 -14165, 2001

  11. Kumar S, Tsai C-J, NussinovR.
      Maximal Stabilities of Reversible Two-State Proteins.
      Biochemistry, 41 (17), 5339-5374, 2001

  12. Gromiha MM, Thomas S, Santhosh C
      Role of cation-pi interactions to the stability of thermophilic proteins
      PREPARATIVE BIOCHEMISTRY & BIOTECHNOLOGY 32 (4): 355-362 2002

  13. Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A.
      Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations.
      Biopolymers 2002 Aug 5;64(4),210-20

  14. Guerois R, Nielsen JE, Serrano L.
      Predicting changes in the stability of proteins and protein complexes:a study of more than 1000 mutations..
      J Mol Biol 2002 Jul 5;320(2):369-87

  15. Kortemme T,Baker D.
      A simple physical model for binding energy hot spots in protein-protein complexes.
      Proc Natl Acad Sci USA 99, 14116-14121, 2002.

  16. Zhou H, Zhou Y.
      Stability scale and atomic solvation parameters extracted from 1023 mutation experiments.
      Proteins 2002 Dec 1;49(4):483-92

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

  18. Gromiha MM
      Factors influencing the thermal stability of buried protein mutants
      POLYMER 44 (14): 4061-4066 JUN 2003

  19. Ahmad S, Gromiha MM, Sarai A
      Real value prediction of solvent accessibility from amino acid sequnce
      PTOTEINS-STRUCTURE FUNCTION AND GENETICS 50 (4): 629-635 MAR 1 2003

  20. Selvaraj S, Gromiha MM
      Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)(8) barrel proteins
      BIOPHYSICAL JOURNAL 84 (3): 1919-1925 MAR 2003

  21. Benjamin J. McFarland, Tanja Kortemme,Shuyuarn F. Yu, David Baker and Roland K. Strong.
      Symmetry Recognizing Asymmetry: Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands.
      Structure 2003, 11 (4), 411-422.

  22. Khatun J, Khare SD, Dokholyan NV.
      Can contact potentials reliably predict stability of proteins?
      J Mol Biol. 2004 Mar 5; 336(5):1223-38

  23. Capriotti E, Fariselli P, Casadio R.
      A neural-network-based method for predicting protein stability changes upon single point mutations.
      Bioinformatics. 2004 Aug 4;20 Suppl 1:I63-I68.

  24. Cuff AL, Martin ACR
      Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein
      JOURNAL OF MOLECULAR BIOLOGY 344 (5):1199-1209 DEC 10 2004

  25. Bastolla U, Moya A, Viguera E, et al.
      Genomic determinants of protein folding thermodynamics in prokaryotic organisms
      JOURNAL OF MOLECULAR BIOLOGY 343 (5):1451-1466 NOV 5 2004

  26. Kumar S, Nussinov R
      Experiment-guided thermodynamic simulations on reversible two-state protein:implications for protein thermostability
      BIOPHYSICAL CHEMISTRY 111(3):235-246 NOV 1 2004

  27. Bordner AJ, Abagyan RA
      Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 57(2):400-413 NOV 1 2004

  28. Chan CH, Liang HK, Hsiao NW, et al.
      Relationship between local structural entropy and protein thermostability
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 57(4):684-691 DEC 1 2004

  29. Sridharan S, Razvi A, Scholtz JM, Sacchettini JC.
      The HPr proteins from the thermophile Bacillus stearothermophilus can form domain-swapped dimers.
      J Mol Biol. 2005 Feb 25;346(3):919-31. Epub 2004 Dec 23.

  30. Jesse D. Bloom, Jonathan J. Silberg, Claus O. Wilke, Allan Drummond, Christoph Adami, and Frances H. Arnold
      Thermodynamic prediction of protein neutrality
      Proc. Natl. Acad. Sci. USA 102, 606-611 (2005).

  31. Bloom JD, Silberg JJ, Wilke CO, et al.
      Thermodynamic prediction of protein neutrality
      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (3): 606-611 JAN 18 2005

  32. Pokala N, Handel TM
      Energy functions for protein design:Adjustment with protein-protein complex affinitiess, models for the unfolded state, and negative design of solubility and specificity
      JOURNAL OF MOLECULAR BIOLOGY 347 (1) : 203-227 MAR 18 2005

  33. Gromiha MM
      Distinct roles of conventional non-covalent and cation-pi interactions in protein stability
      POLYMER 46 (3) : 983-990 JAN 26 2005

  34. Saraboji K, Gromiha MM, Ponnuswamy MN.
      Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes.
      Comput Biol Chem. 2005 Feb;29(1):25-35

  35. Jacobs DJ, Dallaky an S.
      Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity.
      Biophys J. 2005 Feb;88(2):903-15. Epub 2004 Nov 12.

  36. Hamelryck T.
      An amino acid has two sides:A new 2D measure provides a different view of solvent exposure.
      Proteins. 2005 Apr 1;59(1):38-48

  37. Capriotti E, Fariselli P, Casadio R.
      I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or streucture.
      Nucluic Acids Res. 2005 Jul 1:33(Web Serber issue):W306-10.

  38. Hoppe C, Schombrug D. Related Articles, Links
      Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential.
      Protein Sci. 2005 Oct;14(10):2682-92.

  39. Capriotti E, Fariselli P, Calabrese R, Casadio R.
      Predicting protein stability changes from sequences using support vector machines.
      Bioinformatics. 2005 Seq 1;21 Suppl 2:ii54-ii58

  40. Caballero J, Fernandez L, Abreu JI, Fernandez M.
      Amino Acid sequence autocorrelation vectors and ensembles of bayesian-regularized genetic neural networks for prediction of conformational stability of human lysozyme mutants.
      J Chem Inf Model. 2006 May-Jun;46(3):1255-68.

  41. Saraboji K, Gromiha MM, Ponnuswamy MN
      Average assignment method for predicting the stability of protein mutants.
      Biopolymers. 2006 May;82(1):80-92

  42. Cheng JL, Randall A, Baldi P
      Prediction of protein stability changes for single-site mutations using support vector machines.
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 62(4): 1125-1132 MAR 1 2006

  43. Parthiban V, Gromiha MM, Schomburg D
      CUPSAT: prediction of protein stability upon point mutations
      NUCLEIC ACIDS RESEARCH 34: W239-W242 Sp. Iss. SI JUL 1 2006

  44. Sanchez IE, Tejero J, Gomez-Moreno C, et al.
      Point mutations in protein globular domains: Contributions from function, stability and misfolding
      JOURNAL OF MOLECULAR BIOLOGY 363 (2): 422-432 OCT 20 2006

  45. Singh YH, Gromiha MM, Sarai A, et al.
      Atom-wise statistics and prediction of solvent accessibility in proteins
      BIOPHYSICAL CHEMISTRY 124 (2): 145-154 NOV 20 2006

  46. Huang LT, Gromiha MM, Hwang SF, et al.
      Knowledge acquisition and development of accurate rules for predicting protein stability change
      COMPUTATIONAL BIOLOGY AND CHEMISTRY 30 (6): 408-415 DEC 2006

  47. Parthiban V, Gromiha MM, Hoppe C, et al.
      Structural analysis and prediction of protein mutant stability using distance and torsion potentials: Role of secondary structure and solvent accessibility
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 66 (1): 41-52 JAN 2007

  48. Prajapati RS, Das M, Sreeramulu S, et al.
      Thermodynamic effects of proline introduction on protein stability
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 66 (2): 480-491 FEB 1 2007

  49. Huang LT, Saraboji K, Ho SY, Hwang SF, Ponnuswamy MN, Gromiha MM.
      Prediction of protein mutant stability using classification and regression tool
      BIOPHYSICAL CHEMISTRY 125 (2-3): 462-470 FEB 2007

  50. Huang LT, Gromiha MM, Ho SY
      Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model
      JOURNAL OF MOLECULAR MODELING 13 (8): 879-890 AUG 2007

  51. Bueno M, Camacho CJ, Sancho J
      SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 68 (4): 850-862 SEP 2007

  52. Huang LT, Gromiha MM, Ho SY
      iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
      BIOINFORMATICS 23 (10): 1292-1293 MAY 15 2007

  53. Zeldovich KB, Chen PQ, Shakhnovich EI
      Protein stability imposes limits on organism complexity and speed of molecular evolution
      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (41): 16152-16157 OCT 9 2007

  54. Parthiban V, Gromiha MM, Abhinandan M, et al.
      Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development
      BMC STRUCTURAL BIOLOGY 7: Art. No. 54 AUG 16 2007

  55. Deutsch C, Krishnamoorthy B
      Four-body scoring function for mutagenesis
      BIOINFORMATICS 23 (22): 3009-3015 NOV 15 2007

  56. Fernandez M, Caballero J, Fernandez L, et al.
      Classification of conformational stability of protein mutants from 2D graph representation of protein sequences using support vector machines
      MOLECULAR SIMULATION 33 (11): 889-896 2007

  57. Masso M, Vaisman II
      Accurate prediction of enzyme mutant activity based on a multibody statistical potential
      BIOINFORMATICS 23 (23): 3155-3161 DEC 1 2007

  58. Fernandez M, Abreu JI, Caballero J, et al.
      Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants using amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesianregularized genetic neural networks
      MOLECULAR SIMULATION 33 (13): 1045-1056 2007

  59. Fernandez M, Caballero J, Fernandez L, et al.
      Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: Chymotrypsin inhibitor 2 mutants
      JOURNAL OF MOLECULAR GRAPHICS & MODELLING 26 (4): 748-759 NOV 2007

  60. Folch B, Rooman M, Dehouck Y
      Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials
      JOURNAL OF CHEMICAL INFORMATION AND MODELING Volume: 48 Issue: 1 Pages: 119-127 Published: JAN 2008
      

  61. Shen BR, Bai JW, Vihinen M
      Physicochemical feature-based classification of amino acid mutations
      PROTEIN ENGINEERING DESIGN & SELECTION Volume: 21 Issue: 1 Pages: 37-44 Published: JAN 2008
      

  62. Tan YH, Luo R
      Protein stability prediction: A Poisson-Boltzmann approach
      JOURNAL OF PHYSICAL CHEMISTRY B Volume: 112 Issue: 6 Pages: 1875-1883 Published: FEB 14 2008
      

  63. Istomin AY, Gromiha MM, Vorov OK, et al.
      New insight into long-range nonadditivity within protein double-mutant cycles
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Volume: 70 Issue: 3 Pages: 915-924 Published: FEB 15 2008
      

  64. Grandison S, Morris RJ
      Biological pathway kinetic rate constants are scale-invariant
      BIOINFORMATICS, 24 (6):741-743, Mar 2008
      

  65. Schmidt am Busch M, Lopes A, Amara N, et al.
      Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design
      BMC BIOINFORMATICS, 9 Number: 148, Mar 13 2008
      

  66. Stout M, Bacardit J, Hirst JD, et al.
      Prediction of recursive convex hull class assignments for protein residues
      BIOINFORMATICS, 24(7): 916-923, Apr 2008
      

  67. Bolen DW, Rose GD
      Structure and energetics of the hydrogen-bonded backbone in protein folding
      ANNUAL REVIEW OF BIOCHEMISTRY, 77: 339-362, 2008
      

  68. Capriotti E, Fariselli P, Rossi I, et al.
      Conference Information: Annual Meeting of the Italian-Society-of-Bioinformatics, APR 26-28, 2007 Naples, ITALY
      BMC BIOINFORMATICS, 9: S6, Suppl. 2, 2008
      

  69. Rajasekaran R, Doss CGP, Sudandiradoss C, et al.
      Effect of deleterious nsSNP on HER2 receptor based on stability and binding affinity with herceptin: A computational approach
      COMPTES RENDUS BIOLOGIES, 331 (6): 409-417 Published: JUN 2008
      

  70. Kamisetty H, Xing EP, Langmead CJ
      Free energy estimates of all-atom protein structures using generalized belief propagation Conference Information: 11th Annual International Conference on Research in Computational Molecular Biology, APR 21-25, 2007 Oakland, CA
      JOURNAL OF COMPUTATIONAL BIOLOGY, 15(7):755-766, Sep 2008
      

  71. Masso M, Vaisman II
      Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
      BIOINFORMATICS, 24 (18): 2002-2009, Sep 2008
      

  72. Ahmad S, Keskin O, Sarai A, et al.
      Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
      NUCLEIC ACIDS RESEARCH, 36 (18): 5922-5932, Oct 2008
      

  73. Gromiha MM, Huang LT, Lai LF
      Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins 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 Volume: 5265 Pages: 1-12 Published: 2008
      

  74. Radestock S, Gohlke H
      Exploiting the Link between Protein Rigidity and Thermostability for Data-Driven Protein Engineering
      ENGINEERING IN LIFE SCIENCES, 8 ( 5): 507-522, Oct 2008
      

  75. Bougouffa S, Warwicker J
      Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces
      BMC BIOINFORMATICS, 9: 448 Published: OCT 21 2008
      

  76. Biswas S, Guharoy M, Chakrabarti P
      Dissection, residue conservation, and structural classification of protein-DNA interfaces
      PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74 (3):643-654, Feb 2009
      

  77. Kang S, Chen G, Xiao GF
      Robust prediction of mutation-induced protein stability change by property encoding of amino acids
      PROTEIN ENGINEERING DESIGN & SELECTION, 22 (2): 75-83, Feb 2009
      

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

  79. Huang LT, Gromiha MM
      Reliable prediction of protein thermostability change upon double mutation from amino acid sequence
      BIOINFORMATICS, 25 (17) : 2181-2187, Sep 2009
      

  80. Potapov V, Cohen M, Schreiber G
      Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
      PROTEIN ENGINEERING DESIGN & SELECTION, 22 (9): 553-560, Sep 2009
      

  81. Dehouck Y, Grosfils A, Folch B, et al.
      Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0
      BIOINFORMATICS, 25 (19): 2537-2543, Oct 2009
      

• Databases

  1. Chiu WLAK, Sze CN, Ip LN, Chan SK, Au-Yeung SCF
     NTDB: Thermodynamic Database for Nucleic Acids
     NUCLEIC ACIDS RES 29 (1): 230-233 JAN 1 2001

  2. Eyal E, Najmanovich R, Sobolev V, Edelman M
     MutaProt: a web interface for structural analysis of point mutations
     BIOINFORMATICS 17 (4): 381-382 APR 2001

  3. Parabakaran P, An JH, Gromiha MM, et al.
     Thermodynamic database for protein-nucleic acid interactions (ProNIT)
     BIOINFORMATICS 17 (11) : 1027-1034 NOV 2001

  4. Dosztanyi Z, Magyar C, Tusnady G, Simon I.
     SCide:identification of stabilization centers in proteins
     BIOINFORMATICS 2003 May 1;19(7):899-900

  5. Shir-Ly Huang, Li-Cheng Wu, Han-Kuen Liang, Kuan-Ting Pan, Jorng-Tzong Horng and Ming-Tat Ko
     PGTdb: a database providing growth temperatures of prokaryotes
     Bioinformatics 20(2): 276-278 (2004)

  6. McSparron H, Blythe MJ, Zygouri C,Doytchinova IA, Flower DR.
     JenPep: a novel computational information resource for immunobiology and vaccinology.
     J Chem Inf Comput Sci. 2003 Jul-Aug;43(4);1276-87

  7. Ahmad S, Gromiha M, Rawareh H, et al.
     ASA View:Database and tool for solvent accessibility representation in protein
     BMC BIOINFORMATICS 5: Art. No. 51 MAY 1 2004

  8. Fulton KF, Devlin GL, Jodun RA, Silvestri L, Bottomley SP, Fersht AR, Buckle AM.
     PFD:a database for the investigation of protein folding kinetics and stability.
     Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D279-83.

  9. Buckingham SD, Pym L, Jones AK, Brown L, Sansom MS, Sattelle DB,Biggin PC.
     A7DB: a relational database for mutational, physiological and pharmacological data related to the aplha7 nicotinic acetylcholine receptor.
     BMC Neurosci. 2005 Jan 20;6(1):2

  10. Neshich G, Borro LC, Higa RH, et al.
      The diamond STING server
      NUCLEIC ACIDS RESEARCH 33: W29-W35 Suppl. 2 JUL 1 2005

  11. Gromiha MM, Yabuki Y, Suresh MX, et al.
      TMFunction: database for functional residues in membrane proteins
      NUCLEIC ACIDS RESEARCH, 37: Sp. Iss. SI: D201-D204, Jan 2009

  12. Lonquety M, Lacroix Z, Papandreou N, et al.
      SPROUTS: a database for the evaluation of protein stability upon point mutation
      NUCLEIC ACIDS RESEARCH, 37: Sp. Iss. SI: D374-D379, Jan 2009

• Comparing experimental data

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

• Reviews

1. Cooper A
   Thermodynamic analysis of biomolecular interactions
   CURR OPIN CHEM BIOL 3 (5): 557-563 OCT 1999 (* SPECIAL INTEREST)

2. Oda N, Nakamura H
   Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition
   GENES CELLS 5 (5): 319-326 MAY 2000

3. Gilis, D., Wintjens, R and Rooman, M
   Computer-aided methods for evaluating thermodynamic and thermal stability changes of proteins
   Rec. Res. Devel. Prot. Eng. 1, 277-290 (2001)

4. Saven J
   Combinatorial protein design.
   Curr Opin Struct Biol 2002 Aug;12(4):453

5. Mendes J,Guerois R,Serrano L.
   Energy estimation in protein design.
   Curr Opin Struct Biol 2002 Aug;12(4):441 (* Special interest)

6. Oliviero Carugo and Sandor Pongor
   The evolution of structural databases.
   Trends in Biotechnology 20 (12), 498-501 DEC 2002.

7. Dubravko Jeli,Tibor Toth and Donatella Verbanac
   Macromolecular Databases A Background of Bioinformatics
   Food Technol. Biotechnol. 41(3) 269-286 (2003)

8. Gromiha MM, Selvaraj S.
   Inter-residue interactions in protein folding and stability.
   Prog Biophys Mol Biol. 2004 Oct;86(2):235-77.

9. Gromiha MM, Ahmad S.
   Role of solvent accessiblity in structure based drug design
   Curr. Comput. Aided Drug Des. 2005, 1, 223-235.

10. HarshaRani GV, Vayttaden SJ, Bhalla US.
    Electronic data sources for kinetic models of cell signaling
    J Biochem (Tokyo). 2005 Jun;137(6):653-7.

11. Schueler-Furman O, Wang C, Bradley P, et al.
    Progress on modeling of protein structures and interactions
    SCIENCE 310 (5748):638-642 OCT 28 2005

12. Arauzo-Bravo MJ, Ahmad S
    Protein sequence and structure database : A review
    CURRENT ANALYTICAL CHEMISTRY 1 (3) : 355-371 NOV 2005

13. Gromiha MM
    Prediction of protein stability upon point mutations
    BIOCHEMICAL SOCIETY TRANSACTIONS Volume: 35 Pages: 1569-1573 Part: Part 6 Published: DEC 2007
    

14. Zeldovich KB, Shakhnovich EI
    Understanding protein evolution: From protein physics to Darwinian selection
    ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 59: 105-127, 2008
    

15. Chen YW, Ding F, Nie HF, et al.
    Protein folding: Then and now
    ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 469 (1): 4-19, Jan 2008
    

16. Tuncbag N, Kar G, Keskin O, et al.
    A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
    BRIEFINGS IN BIOINFORMATICS, 10 (3): 217-232, May 2009
    

17. Gromiha MM
    Revisiting "Reverse Hydrophobic Effect": Applicable Only to Coil Mutations at the Surface
    BIOPOLYMERS, 91 (7): 591-599, Jul 2009
    

• 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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