CRASP

Related papers

Papers on correlations of amino acid substitutions and related problems.

(Updated 09.07.2004)

        

  1.  Altschuh,D., Lesk,A.M., Bloomer,A.C. and Klug,A. (1987) Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J. Mol. Biol., 193, 693-707.
  2.  Altschuh,D., Vernet,T., Berti,P., Moras,D. and Nagai,K. (1988) Coordinated amino acid changes in homologous protein families. Protein Eng., 2, 193-199.
  3.  Atchley,W.R., Wollenberg,K.R., Fitch,W.M., Terhalle,W., Dress,A.W. (2000) Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol. 17, 164-78.
  4.  Benner,S.A. and Gerloff,D. (1991) Patterns of divergence in homologous proteins as indicators of secondary and tertiary structures: the catalytic domain of protein kinases. Advan. Enzyme Regulat., 31, 121-181.
  5.  Berger,B, Wilson,D.B., Wolf,E., Tonchev,T., Milla,M. and Kim,P.S. (1995) Predicting coiled coils by use of pairwise residue correlations. Proc. Natl. Acad. Sci. U S A, 92, 8259-8263.
  6.  Berger,B. (1995) Algorithms for protein structural motif recognition. J. Comput. Biol. 2, 125-138.
  7.  Chelvanayagam,G., Eggenschwiler,A., Knecht,L., Gonnet.,G. and Benner,S. (1997) An analysis of simultaneous variation in protein structures. Prot. Eng., 10, 307-316.
  8.  Clarke,N.D. (1995) Covariation of residues in homeodomain sequence family. Prot. Sci., 4, 2269-2278.
  9.  Eisenhaber,B., Bork,P. and Eisenhaber,F. (1999) Prediction of potential GPI-modification sites in proprotein sequences. J. Mol. Biol., 292, 741-58. See also WWW site at http://mendel.imp.univie.ac.at/sat/gpi/gpi_prediction.html
  10.  Eisenhaber,B., Bork,P., Eisenhaber F. (1998) Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. Protein Eng., 11, 1155-1161.
  11. Fukami-Kobayashi,K., Schreiber,D.R., Benner,S.A. (2002)  Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J. Mol. Biol., 319, 729-743.
  12.  Gerstein,M., Sonnhammer,E.L. and Chothia,C. (1994) Volume changes in protein evolution. J. Mol. Biol., 236, 1076-1078.
  13.  Giraud,B.G., Lapedes,A. and Liu, L.C. (1998) Analysis of correlations between sites in models of protein sequences. Phys. Rev. E, 58, 6312-6322.
  14.  Gobel,U., Sander,C., Schneider,R. and Valencia,A. (1994) Correlated mutations and residue contacts in proteins. Prot. Struct. Funct. Genet., 18, 309-317.
  15.  Hoffman.N.G., Schiffer,C.A., Swanstrom,R. (2003) Covariation of amino acid positions in HIV-1 protease. Virology. 314,536-548.
  16.  Kimura,M. (1991) Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics. Proc. Natl. Acad. Sci. USA, 88, 5969-5973.
  17.  Kondrashov,A.S., Sunyaev,S., Kondrashov,F.A. (2002) Dobzhansky-Muller incompatibilities in protein evolution. Proc. Natl. Acad. Sci. USA, 99, 14878-14883.
  18.  Korber,B.T.M., Farber,R.M., Wolpert,D.H. and Lapedes,A.S. (1993) Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA, 90, 7176-7180.
  19.  Kreisberg,R., Buchner,V. and Arad,D. (1995) Paired natural cysteine mutation mapping: aid to constraining models of protein tertiary structure. Protein Sci., 4, 2405-2410.
  20.  Lapedes,A.S., Giraud,B.G., Liu,L.C. and Stormo,G.D. (1997) Correlated mutations in protein sequences: phylogenetic and structural effects. In Proceedings of the AMS/SIAM Conference on Statistics in Molecular Biology, Vol. 33, Monograph Series of the Institute for Mathematical Statistics, Hayward, CA, pp. 236–256.
  21.  Larson,S.M., Di Nardo,A.A., Davidson,A.R. (2000) Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol., 303, 433-446.
  22.  Lim,V.I. and Ptitsyn,O.B. (1970) On the constancy of the hydrophobic nucleus volume in molecules of myoglobins and hemoglobins. Mol. Biol. (USSR), 4, 372-382.
  23.  Lockless,S.W. and Ranganathan,R. (1999) Evolutionary conserved pathways of energetic connectivity in protein families. Science, 286, 295-299.
  24.  Mamitsuka,H. (1995) Representing inter-residue dependencies in protein sequences with probabilistic networks. CABIOS, 11, 413-422.
  25.  Mandel-Gutfreund,Y., Zaremba,S.M., Gregoret,L.M. (2001) Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands. J. Mol. Biol., 305, 1145-1159.
  26.  Nagl,S.B. (2001) Can correlated mutations in protein domain families be used for protein design? Brief Bioinform., 2, 279-288.
  27.  Nagl,S.B., Freeman,J., Smith,T.F. (1999) Evolutionary constraint networks in ligand-binding domains: an information-theoretic approach. Pac. Symp. Biocomput., 90-101
  28.  Neher,E. (1994) How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. USA, 91, 98-102.
  29.  Olmea,O., Rost,B., Valencia,A. (1999) Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol., 293, 1221-1239.
  30.  Oliveira,L., Paiva,A.C.,Vriend.G. (2002) Correlated mutation analyses on very large sequence families. Chembiochem., 3, 1010-1017.
  31.  Ortiz,A.R., Kolinski,A. and Skolnick,J. (1998) Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignment. J. Mol. Biol., 277, 419-448.
  32.  Pazos,F., Helmer-Citterich,M., Ausiello,G. and Valencia,A. (1997a) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
  33.  Pazos,F., Olmea,O. and Valencia,A. (1997b) A graphical interface for correlated mutations and other protein structure prediction methods. CABIOS, 13, 319-321.
  34.  Pollock,D.D. and Taylor,W.R. (1997) Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Prot. Eng., 10, 647-657.
  35.  Pollock,D.D., Taylor,W.R. and Goldman N. (1999) Coevolving protein residues: maximum likelihood identefication and relationship to structure. J. Mol. Biol., 287, 187-198.
  36.  Pritchard,L. and Dufton,M.J. (2000) Do proteins learn to evolve? The Hopfield network as a basis for the understanding of protein evolution. J.Theor.Biol., 202, 77-86.
  37.  Ptitsyn,O.B. and Volkenstein,M.V. (1986) Protein structures and the neutral theory of evolution. J. Biomol. Struct. Dynam., 4, 137-156.
  38.  Shindyalov,I.N., Kolchanov,N.A. and Sander,C. (1994) Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Prot. Eng., 7, 349-358.
  39.  Taylor,W.R. and Hatrick,K. (1994) Compensating changes in protein multiple sequence alignment. Prot. Eng., 7, 341-348.
  40.  Thomas,D.J., Casari,G. and Sander,C. (1996) The prediction of protein contacts from multiple sequence alignments. Prot. Eng., 9, 941-948.
  41.  Tillier,E.R.M. and Lui,T.W.H. (2003) Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics, 19, 750-755 . (see also program Dependency )
  42. Tuff P, Darlu P. (2000) Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol. Biol. Evol., 17,  1753-1759.
  43.  Wollenberg,K.R. and Atchley,W.R. (2000) Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. USA, 97, 3288-3291.

    44.  

Experimental evidences of cooperativity of residue substitutions effects:

    

  1. Carter,P.J., Winter,G., Wilkinson,A.J. and Fersht,A. (1984) The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell, 38, 835-840.
  2. Desjarlais,J.R., Berg,J.M. (1992) Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach. Proteins, 12,101-4.
  3. Mateu,M.G. and Fersht,A.R. (1999) Mutually compensatory mutations during evolution of the tetramerization domain of tumor supressor p53 lead to impaired hetero-oligomerization. Proc. Natl. Acad. Sci. USA, 96, 3595-3599.
  4. Vernet,T., Tessier,D.C., Khouri,H.E. and Altschuh,D. (1992) Correlation of co-ordinated amino acid changes at the two-domain interface of cysteine proteases with protein stability. J. Mol. Biol., 224, 501-509.
  5. Yanofsky,C., Horn,V., Thorpe,D. (1964) Protein structure relationships revealed by mutation analysis. Science, 146, 1593-1594.
  6. Jespers,L., Lijnen,H.R., Vanwetswinkel,S., Van Hoef,B., Brepoels,K., Collen,D., De Maeyer,M. (1999) Guiding a docking mode by phage display: selection of correlated mutations at the staphylokinase-plasmin interface. J. Mol. Biol., 290, 471-479.
  7. Lockless,S.W. and Ranganathan,R. (1999) Evolutionary conserved pathways of energetic connectivity in protein families. Science, 286, 295-299.

   

Our publications:

Dmitry A. Afonnikov and Nikolay A. Kolchanov (2004) CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucl. Acids. Res.,  32, W64-W68. [Abstract] (The article is free from NAR 2004 Web server issue page). 

Valuev,V.P., Afonnikov,D.A., Ponomarenko,M.P., Milanesi,L., Kolchanov,N.A. (2002) ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res., 30, 200-202. (This database contain results of correlation analysis of multiple sequence alignments by CRASP program.)

Afonnikov,D.A., Oshchepkov,D.Y., Kolchanov,NA. (2001) Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics, 17, 1035-1046.

Afonnikov,D.A., Kolchanov,N.A. (2001) The conserved characteristics of DNA-binding domains belonging to the homeodomain class that are associated with coadaptive substitutions of amino acid residues. Dokl. Biochem. Biophys., 380, 352-355.

Afonnikov,D.A and Titov,I.I. (1998) Functional relationship between amino acid residues at n- and c-termini of DNA-binding regions of transcription factors CREB and AP-1 revealed by analyzing the pair correlations of amino acid substitutions. Proc. 1st Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 377-379 .

Afonnikov,D.A. and Wingender,E. (1998) Statistical relation between the positions of the alpha-helix in the zinc-finger DNA-binding domain: results from the phage display data analysis. Proc. 1st Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 380-383 .

Afonnikov,D.A., Kondrakhin,Yu.V. and Titov,I.I. (1997) Revealing of correlated positions of the DNA-binding region of the CREB and AP-1 transcription factor families. Mol. Biol. (Russian), 31, 741-748.

See also CRASP2001 presentation. 

Related www-links

Bibliography on Studies of Correlation Structures of DNA Sequences (some papers also deal with correlations in protein sequences ); compiled and maintained by Wentian_Li .

 "big-Pi" predictor (Eisenhaber,B., Bork,P. and Eisenhaber,F.)

 Dependency program site by Elisabeth R. M. Tillier and Thomas W. H. Lui.

 

CRASP main page