Data updated: Feb. 22 2013

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What's new in ProTherm

  • Data updated. New entries in this update are from 25979 to 26045. (Feb. 22, 2013).

  • Data updated. New entries in this update are from 25845 to 25978. (Nov. 8, 2012).

  • Data updated. New entries in this update are from 25617 to 25844. (July 31, 2012).

  • Data updated. New entries in this update are from 25499 to 25616. (Dec. 21, 2011).

  • Data updated. New entries in this update are from 25294 to 25498. (Apr. 27, 2011).

  • Data updated. New entries in this update are from 25101 to 25293. (Mar. 30, 2011).

  • Data updated. New entries in this update are from 25001 to 25100. (Feb. 17, 2011).

  • Direct linking from PDB to ProTherm entries: (Aug. 17, 2010).

    You can link from structural information to corresponding ProTherm entries by using URL:
    http://www.abren.net/protherm/protherm_pdburl.php?ENTRY=****
    where **** corresponds to 4-letter PDB ID. You can also specify multiple PDB IDs separated by comma. Once this information is sent to ProTherm, the program automatically finds homologues of the structure (95% identity and higher), and display the list of corresponding ProTherm entries with some essential information.

  • Data updated. New entries in this update are from 24896 to 25000. (Aug. 17, 2010).

  • Data updated. New entries in this update are from 24790 to 24895. (June 29, 2010).

  • Data updated. New entries in this update are from 24680 to 24789. (May 26, 2010).

  • Addition of 'ADDITIVES' field: So far, the information about additives in solutions has been described in REMARKS field. We added a new field ADDITIVES for the additives information. (Apr. 28, 2010).

  • Data updated. New entries in this update are from 24486 to 24679. (Mar. 31, 2010).

  • Data updated. New entries in this update are from 24389 to 24485. (Feb. 5, 2010).

  • Data updated. New entries in this update are from 24287 to 24388. (Dec. 24, 2009).

  • Data updated. New entries in this update are from 24178 to 24286. (Nov. 30, 2009).

  • Data updated. New entries in this update are from 23989 to 24177. (Oct. 21, 2009).

  • Data updated. New entries in this update are from 23862 to 23988. (July 2, 2009).

  • Data updated. New entries in this update are from 23799 to 23861. (May 29, 2009).

  • Data updated. New entries in this update are from 23682 to 23798. (Dec. 19, 2008).

  • Data updated. New entries in this update are from 23318 to 23581. (Sept. 8, 2008).

  • Data updated. New entries in this update are from 23115 to 23317. (July 4, 2008).

  • Data updated. New entries in this update are from 22914 to 23114. (May 15, 2008).

  • Data updated. New entries in this update are from 22714 to 22913. (Apr. 10, 2008).

  • Data updated. New entries in this update are from 22504 to 22713. (Feb. 18, 2008).

  • Data updated. New entries in this update are from 22287 to 22503. (Jan. 25, 2008).

  • Data updated. New entries in this update are from 22077 to 22286. (Dec. 25, 2007).

  • Data updated. New entries in this update are from 21893 to 22076. (Nov. 21, 2007).

  • Data updated. New entries in this update are from 21389 to 21892. (Sept. 28, 2007).

  • Data updated. New entries in this update are from 21040 to 21388. (Aug. 29, 2007).

  • Data updated. New entries in this update are from 20665 to 21039. (July 25, 2007).

  • Data updated. New entries in this update are from 20477 to 20664. (May 29, 2007).

  • Data updated. New entries in this update are from 20278 to 20476. (Apr. 16, 2007).

  • Regarding signs of ddG and ddG_H2O, we checked a set of articles to make sure the signs are entered correctly as per our definition and found the signs are correct. For more details, please see Known problems (Feb. 28, 2007)

  • Data updated. New entries in this update are from 20116 to 20277. (Feb. 16, 2007).

  • Data updated. New entries in this update are from 19945 to 20115. (Nov. 16, 2006).

  • Data updated. New entries in this update are from 19748 to 19944. (Oct. 24, 2006).

  • Data updated. New entries in this update are from 19539 to 19747. (Aug. 29, 2006).

  • Data updated. New entries in this update are from 19308 to 19538. (July 27, 2006).

  • Data updated. New entries in this update are from 19104 to 19307. (June 29, 2006).

  • Data updated. New entries in this update are from 18885 to 19103. (May 26, 2006).

  • Data updated. New entries in this update are from 18738 to 18884. (April 12, 2006).

  • Data updated. New entries in this update are from 17312 to 18737. (Sept. 20, 2005).

  • Data updated. New entries in this update are from 16803 to 17311. (Aug. 3, 2005)

  • Cross-link with STING: ProTherm entries are linked to STING server, which provides comprehensive analysis of a relationship between protein sequence, structure, function and stability. PDB column in ProTherm is linked to STING sequence frame and Java Protein Dosssier (JPD), Mutation column is linked to JPD and STING Report, which is an exhaustive presentation of the structure/function descriptors for particular residues, and Secondary Structure column is linked to PDB Cartoon. Also, for given protein mutations searched within STING, each entry in STING Report is linked to available thermodynamic data in ProTherm. These cross-references would help users to analyze the relationship between structure and thermodynamics of proteins. (July 15, 2005)

  • Data updated. New entries in this update are from 16604 to 16802. (June. 8, 2005)

  • Data updated. New entries in this update are from 16277 to 16603. (Mar. 15, 2005)

  • Data updated. New entries in this update are from 16101 to 16276. (Dec. 14, 2004)

  • Data updated. New entries in this update are from 15907 to 16100. (Oct. 6, 2004)

  • Data updated. New entries in this update are from 15521 to 15906. (Aug. 19, 2004)

  • Data updated. New entries in this update are from 15103 to 15518. (Mar. 25, 2004)
    PIR code is included for Display option in ProTherm Search page.
    PMID number is provided with REFERENCE so that the reference is directly linked to PubMed.

  • Data updated. New entries in this update are from 14583 to 15102. (Dec. 11, 2003)

  • Data updated. New entries in this update are from 14301 to 14582. (Sept. 5, 2003)

  • Data updated. New entries in this update are from 13701 to 14300. (June 18, 2003)
    This update mainly contain the data of unfolding free energy(DG),unfolding free-energy change due to mutation (DDG),etc separated from old entries as they are at different temparature compare to remaining parameters. For more details, please see Known Problems.

  • Data updated. New entries in this update are from 13141 to 13700. (May 9, 2003)

  • Data updated. New entries in this update are from 12278 to 13140. (Mar. 17, 2003)

  • Addition of Related Entries. Each article usually contains multiple data and they are entered in different entries. Also, because of the separation of Tm data and DG/DDG data, some data are entirely separated. In order to put together all the data in the same article, we added a new field RELATED_ENTRIES. Users can view all the related entries by clicking the entry number in this field. (Dec. 9, 2002)

  • Separation of Tm data and DG/DDG data. So far, we have included Tm data and DG/DDG/DH data in the same entry. However, the DG/DDG/DH data are often extrapolated at room temperature or other temperatures. We have placed all the temperatures at Tm field without distinguishing T from Tm for thermal denaturation experiments (see Known Problems). This has been causing confusions. So, we have separated these data and placed the extrapolated temperature in a new T filed. Please note that, because of this separation, some of the separated DG/DDG/DH data will be uploaded in the database later. (Dec. 9, 2002)

  • Data updated. New entries in this update are from 11765 to 12277. (Dec. 9, 2002)

  • Energy unit of DH(DDH), DG(DDG),DCp can be selected from kcal and kj before search.(July. 17, 2002)

  • Temperature unit of T and DTm can be selected from C (Celsius) and K (Kelvin). (July. 17, 2002)

  • Molecular weight is added in Search Option. Molecular weight and amino acid length are added in Display Option. Molecular weights were calculated as follows: The amino acid sequence corresponding to a protein was taken from PIR database, and leader (signal) regions were removed. Then, the molecular weights were calculated according to the amino acid sequence. Amino and carboxy terminals were taken into account. Any mutations to the amino acid sequence were taken into account. However, post-translational modifications were NOT taken into account. ( July. 17, 2002)

  • Data updated. New entries in this update are from 10791 to 11764.( July. 17, 2002)

  • Cross-References from PDB, PIR and SWISS-PROT to ProTherm. We have supplied tables to show the correspondence between the database entries of PDB, PIR and SWISS-PROT and ProTherm entries. These tables can be used to create pointers from these database entries to ProTherm. In order to see these tables, go to "Cross-Reference" in the top page.(July 4, 2002)

  • Homologous PDB entries are linked from ProTherm. So far, PDB entries of structures corresponding to ProTherm entries are given, but not all the links are accurate because the source of proteins had not been specified for earlier ProTherm entries. While we now assign unique PDB code for proteins from different species, users may want to know homologous PDB structures. So, this link helps checking those structures. The links show the structures with the percentage of sequence identity higher than 95%. (June 30, 2002)

  • Data updated. New entries in this update are from 11091 to 11311.( May 17, 2002)

  • Data updated. New entries in this update are from 10790 to 11090.( Mar 26, 2002)

  • Data updated. New entries in this update are from 10366 to 10790.( Feb. 25, 2002)

  • Data updated. New entries in this update are from 10106 to 10365. Users can specify a range of entries for search by filling the Entry field in the search page. ( Dec. 6, 2001)

  • A table for the frequency of amino acids in mutation sites was added. This table shows the number of mutations for every combinations of amino acids, counted from ProTherm. (Oct., 2001)

  • The number of entries in ProTherm has reached 10,000. Please see Statistics for more detail. New entries in this update are from 9790 to 10106. Users can specify a range of entries for search by filling the Entry field (e.g., 9790-10106) in the search page. (Oct. 18, 2001)

  • List of Sources of proteins is provided in Statistics page. (June, 2001)

  • lProtein Source can be searched from Advanced Search menu. The Source is also added in the Display Option. (June, 2001)

  • Enthalpy change, dH, is classified into van't Hoff enthalpy change, dHvH, and calorimetric enthalpy change, dHcal. The dHvH values are obtained from the temperature dependence of denaturation equilibrium constant, and the dHcal values can be obtained from calorimetric measurements. (May, 2001)
  • Unique PDB codes are assigned to proteins from different species. Previously, they were not differentiated. (April, 2001)
  • PIR and SWISS-PROT codes are included. (March, 2001)
  • The concentration of protein for each experiment is added. (February, 2001)
  • The source of each protein is included. (February, 2001)
  • E-mails were sent to the corresponding authors of each paper included in ProTherm. We made corrections and modifications to ProTherm according to their suggestions. (January, 2001)
  • PDB code can be used for searching thermodynamic data associated with the structure. (February, 2001)
  • Release of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions. (December 12, 2000)
  • Quick search is provided at the top page of ProTherm. It covers all the character fields in the database. (November, 2000)
  • The number of states in the transition is added, and can be searched. (November, 2000)
  • NMR category is added to the "Measure" item, and can be searched separately. (October, 2000)
  • Link to BRENDA is added. (August, 2000)
  • Reversibility of denaturation is included in the data, and can be searched. (June, 2000)
  • The names and concentrations of buffers and ions are included. (April, 2000)
  • Displaying Mutation Sites in ProTherm. (October 22, 99)
  • Release of ProTherm: Thermodynamic Database for Proteins and Mutants. (September 29, 98)

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