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Shalom Rackovsky, Ph.D.

Shalom Rackovsky, Ph.D.

Contact

Office (585) 275-2235

About Me

Faculty Appointments

Research Associate Professor - Department of Biochemistry and Biophysics (SMD)

Credentials

Education

PhD | Massachusetts Institute of Technology. Chemical Physics. 1972

BA | Yeshiva University. Chemistry. 1967

Research

We are interested in computational studies of protein folding and dynamics, and particularly in the information about protein physics which is available through bioinformatic studies. We have developed a series of novel approaches to protein biophysics based on ideas from information theory and sign...
We are interested in computational studies of protein folding and dynamics, and particularly in the information about protein physics which is available through bioinformatic studies. We have developed a series of novel approaches to protein biophysics based on ideas from information theory and signal processing. In recent work we developed the first bioinformatic representation of protein dynamics, and are currently using this tool, in combination with earlier studies of the static physical properties of amino acid sequences, to elucidate basic mechanisms of protein folding. We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins.
In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. These studies are still ongoing in our group.

Publications

Journal Articles

Global Survey of Protein Dynamic Properties.

Konkankit CC, Rackovsky S

The journal of physical chemistry. B. 2023 June 27 Epub 06/27/2023.

Dynamic and conformational switching in proteins.

Scheraga HA, Rackovsky S

Biopolymers.. 2020 December 3 :e23411. Epub 12/03/2020.

Tribute to Harold A. Scheraga.

Maisuradze GG, Montelione GT, Rackovsky S, Skolnick J

The journal of physical chemistry. B. 2020 November 19124 (46):10301-10302. Epub 10/23/2020.

The structure of protein dynamic space.

Rackovsky S, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 2020 August 18117 (33):19938-19942. Epub 08/05/2020.

Sequence-specific dynamic information in proteins.

Scheraga HA, Rackovsky S

Proteins.. 2019 October 87 (10):799-804. Epub 06/11/2019.

Beyond Supersecondary Structure: Physics-Based Sequence Alignment.

Rackovsky S

Methods in molecular biology.. 2019 1958 :341-346. Epub 1900 01 01.

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.

He Y, Maisuradze GG, Yin Y, Kachlishvili K, Rackovsky S, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 2017 February 14114 (7):1578-1583. Epub 01/31/2017.

Global informatics and physical property selection in protein sequences.

Scheraga HA, Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 2016 February 16113 (7):1808-10. Epub 02/01/2016.

Nonlinearities in protein space limit the utility of informatics in protein biophysics.

Rackovsky S

Proteins.. 2015 November 83 (11):1923-8. Epub 09/10/2015.

Alternative approach to protein structure prediction based on sequential similarity of physical properties.

He Y, Rackovsky S, Yin Y, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 2015 April 21112 (16):5029-32. Epub 04/06/2015.

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences.

Scheraga HA, Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 2014 April 8111 (14):5225-9. Epub 03/24/2014.

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.

Krupa P, Sieradzan AK, Rackovsky S, Baranowski M, O?ldziej S, Scheraga HA, Liwo A, Czaplewski C

Journal of chemical theory and computation.. 2013 October 89 (10)Epub 1900 01 01.

Sequence determinants of protein architecture.

Rackovsky S

Proteins.. 2013 October 81 (10):1681-5. Epub 08/13/2013.

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.

He Y, Mozolewska MA, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, ?lusarz R, Czaplewski CR, O?dziej S, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 2013 September 10110 (37):14936-41. Epub 08/26/2013.

Beyond supersecondary structure: the global properties of protein sequences.

Rackovsky S

Methods in molecular biology.. 2013 932 :107-14. Epub 1900 01 01.

Spectral analysis of a protein conformational switch.

Rackovsky S

Physical review letters.. 2011 June 17106 (24):248101. Epub 06/14/2011.

On the information content of protein sequences.

Rackovsky S, Scheraga HA

Journal of biomolecular structure & dynamics.. 2011 February 28 (4):593-4; discussion 669-674. Epub 1900 01 01.

Fold homology detection using sequence fragment composition profiles of proteins.

Solis AD, Rackovsky SR

Proteins.. 2010 October 78 (13):2745-56. Epub 1900 01 01.

Global characteristics of protein sequences and their implications.

Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 2010 May 11107 (19):8623-6. Epub 04/26/2010.

Information-theoretic analysis of the reference state in contact potentials used for protein structure prediction.

Solis AD, Rackovsky SR

Proteins.. 2010 May 178 (6):1382-97. Epub 1900 01 01.

CFP: a web-server for constructing sequence-based protein conformational flexibility profiles.

Kuznetsov IB, Rackovsky S

Bioinformation.. 2009 October 194 (5):176-8. Epub 10/19/2009.

Sequence physical properties encode the global organization of protein structure space.

Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 2009 August 25106 (34):14345-8. Epub 08/12/2009.

Information and discrimination in pairwise contact potentials.

Solis AD, Rackovsky S

Proteins.. 2008 May 1571 (3):1071-87. Epub 1900 01 01.

Property-based sequence representations do not adequately encode local protein folding information.

Solis AD, Rackovsky S

Proteins.. 2007 June 167 (4):785-8. Epub 1900 01 01.

Characterization of architecture signals in proteins.

Rackovsky S

The journal of physical chemistry. B. 2006 September 28110 (38):18771-8. Epub 1900 01 01.

Improvement of statistical potentials and threading score functions using information maximization.

Solis AD, Rackovsky S

Proteins.. 2006 March 162 (4):892-908. Epub 1900 01 01.

Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations.

Kuznetsov IB, Rackovsky S

Protein science : a publication of the Protein Society.. 2004 December 13 (12):3230-44. Epub 1900 01 01.

Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors.

Kuznetsov IB, Rackovsky S

Proteins.. 2004 February 154 (2):333-41. Epub 1900 01 01.

Similarity between the C-terminal domain of the prion protein and chimpanzee cytomegalovirus glycoprotein UL9.

Kuznetsov IB, Rackovsky S

Protein engineering. 2003 December 16 (12):861-3. Epub 1900 01 01.

On the properties and sequence context of structurally ambivalent fragments in proteins.

Kuznetsov IB, Rackovsky S

Protein science : a publication of the Protein Society.. 2003 November 12 (11):2420-33. Epub 1900 01 01.

Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading.

Kuznetsov IB, Rackovsky S

Proteins.. 2002 November 149 (2):266-84. Epub 1900 01 01.

Optimally informative backbone structural propensities in proteins.

Solis AD, Rackovsky S

Proteins.. 2002 August 1548 (3):463-86. Epub 1900 01 01.

Optimized representations and maximal information in proteins.

Solis AD, Rackovsky S

Proteins.. 2000 February 138 (2):149-64. Epub 1900 01 01.

Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing.

Lee J, Scheraga HA, Rackovsky S

Biopolymers.. 1998 August 46 (2):103-16. Epub 1900 01 01.

"Hidden" sequence periodicities and protein architecture.

Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 1998 July 2195 (15):8580-4. Epub 1900 01 01.

Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor.

Kombo DC, Némethy G, Gibson KD, Rackovsky S, Scheraga HA

Journal of molecular biology.. 1996 March 1256 (3):517-32. Epub 1900 01 01.

Effects on protein structure and function of replacing tryptophan with 5-hydroxytryptophan: single-tryptophan mutants of the N-terminal domain of the bacteriophage lambda repressor.

Kombo DC, Némethy G, Gibson KD, Ross JB, Rackovsky S, Scheraga HA

Journal of protein chemistry.. 1996 January 15 (1):77-86. Epub 1900 01 01.

Computational study of packing a collagen-like molecule: quasi-hexagonal vs "Smith" collagen microfibril model.

Lee J, Scheraga HA, Rackovsky S

Biopolymers.. 1996 40 (6):595-607. Epub 1900 01 01.

On the existence and implications of an inverse folding code in proteins.

Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 1995 July 1892 (15):6861-3. Epub 1900 01 01.

Protein sequence randomness and sequence/structure correlations.

Rahman RS, Rackovsky S

Biophysical journal.. 1995 April 68 (4):1531-9. Epub 1900 01 01.

Prediction of conformation of rat galanin in the presence and absence of water with the use of Monte Carlo methods and the ECEPP/3 force field.

Liwo A, O?dziej S, Ciarkowski J, Kupryszewski G, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA

Journal of protein chemistry.. 1994 May 13 (4):375-80. Epub 1900 01 01.

Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment.

Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA

Protein science : a publication of the Protein Society.. 1993 October 2 (10):1697-714. Epub 1900 01 01.

Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide.

Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA

Protein science : a publication of the Protein Society.. 1993 October 2 (10):1715-31. Epub 1900 01 01.

Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations.

Hao MH, Pincus MR, Rackovsky S, Scheraga HA

Biochemistry.. 1993 September 2132 (37):9614-31. Epub 1900 01 01.

On the nature of the protein folding code.

Rackovsky S

Proceedings of the National Academy of Sciences of the United States of America.. 1993 January 1590 (2):644-8. Epub 1900 01 01.

Effects of compact volume and chain stiffness on the conformations of native proteins.

Hao MH, Rackovsky S, Liwo A, Pincus MR, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 1992 July 1589 (14):6614-8. Epub 1900 01 01.

Correlation of the structure of the transmembrane domain of the neu oncogene-encoded p185 protein with its function.

Brandt-Rauf PW, Rackovsky S, Pincus MR

Proceedings of the National Academy of Sciences of the United States of America.. 1990 November 87 (21):8660-4. Epub 1900 01 01.

Comparison of the predicted structure for the activated form of the P21 protein with the X-ray crystal structure.

Chen JM, Lee G, Brandt-Rauf PW, Murphy RB, Rackovsky S, Pincus MR

Journal of protein chemistry.. 1990 October 9 (5):543-7. Epub 1900 01 01.

Conformations of the central transforming region (Ile 55-Met 67) of the p21 protein and their relationship to activation of the protein.

Chen JM, Lee G, Brandt-Rauf PW, Murphy RB, Gibson KD, Scheraga HA, Rackovsky S, Pincus MR

International journal of peptide and protein research. 1990 September 36 (3):247-54. Epub 1900 01 01.

The structure of the carboxyl terminus of the p21 protein. Structural relationship to the nucleotide-binding/transforming regions of the protein.

Brandt-Rauf PW, Carty RP, Chen JM, Lee G, Rackovsky S, Pincus MR

Journal of protein chemistry.. 1990 April 9 (2):137-42. Epub 1900 01 01.

Quantitative organization of the known protein x-ray structures. I. Methods and short-length-scale results.

Rackovsky S

Proteins.. 1990 7 (4):378-402. Epub 1900 01 01.

Protein comparison and classification: a differential geometric approach.

Rackovsky S, Goldstein DA

Proceedings of the National Academy of Sciences of the United States of America.. 1988 February 85 (3):777-81. Epub 1900 01 01.

Differential geometry and protein conformation. V. Medium-range conformational influence of the individual amino acids.

Rackovsky S, Goldstein DA

Biopolymers.. 1987 July 26 (7):1163-87. Epub 1900 01 01.

Substitutions of proline 76 in yeast iso-1-cytochrome c. Analysis of residues compatible and incompatible with folding requirements.

Ernst JF, Hampsey DM, Stewart JW, Rackovsky S, Goldstein D, Sherman F

The Journal of biological chemistry.. 1985 October 25260 (24):13225-36. Epub 1900 01 01.

On the redox conformational change in cytochrome c.

Rackovsky S, Goldstein DA

Proceedings of the National Academy of Sciences of the United States of America.. 1984 September 81 (18):5901-5. Epub 1900 01 01.

Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S.

Rackovsky S, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 1980 December 77 (12):6965-7. Epub 1900 01 01.

Characterization of multiple bends in proteins.

Isogai Y, Némethy G, Rackovsky S, Leach SJ, Scheraga HA

Biopolymers.. 1980 June 19 (6):1183-210. Epub 1900 01 01.

Influence of ordered backbone structure on protein folding. A study of some simple models.

Rackovsky S, Scheraga HA

Macromolecules.. 1978 11 (1):1-8. Epub 1900 01 01.

Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins.

Rackovsky S, Scheraga HA

Proceedings of the National Academy of Sciences of the United States of America.. 1977 December 74 (12):5248-51. Epub 1900 01 01.