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Volumn 8, Issue 5, 1999, Pages 1001-1009

Feasibility in the inverse protein folding protocol

Author keywords

Knowledge based potential; Minus average operation; Structure prediction; Threading; Weak homology

Indexed keywords

PROTEIN;

EID: 0032903975     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.5.1001     Document Type: Article
Times cited : (6)

References (38)
  • 1
    • 85038184314 scopus 로고    scopus 로고
    • Effect of secondary structure prediction on protein fold recognition and database search
    • Akutsu T, Asai K, Hagiya M, Kuhara S, Miyano S, Nakai K, eds. Tokyo, Japan: Universal Academy Press
    • Alexandrov NN, Solovyev VV. 1996. Effect of secondary structure prediction on protein fold recognition and database search. In. Akutsu T, Asai K, Hagiya M, Kuhara S, Miyano S, Nakai K, eds. Genome informatics 1996. Tokyo, Japan: Universal Academy Press.
    • (1996) Genome Informatics 1996
    • Alexandrov, N.N.1    Solovyev, V.V.2
  • 3
    • 0025341237 scopus 로고
    • Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
    • Bowie JU, Clarke ND, Pabo CO, Sauer T. 1990. Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins 7:257-264.
    • (1990) Proteins , vol.7 , pp. 257-264
    • Bowie, J.U.1    Clarke, N.D.2    Pabo, C.O.3    Sauer, T.4
  • 4
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Lüthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Lüthy, R.2    Eisenberg, D.3
  • 5
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through folding motif
    • Bryant SH, Lawrence CE. 1993. An empirical energy function for threading protein sequence through folding motif. Proteins 16:92-112.
    • (1993) Proteins , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 6
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
    • Bult CJ et al. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 275:1058-1073.
    • (1996) Science , vol.275 , pp. 1058-1073
    • Bult, C.J.1
  • 7
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM. 1987. The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826.
    • (1987) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 8
    • 0029959722 scopus 로고    scopus 로고
    • Failures of inverse folding and threading with gapped alignment
    • Crippen GM. 1996. Failures of inverse folding and threading with gapped alignment. Proteins 26:167-171.
    • (1996) Proteins , vol.26 , pp. 167-171
    • Crippen, G.M.1
  • 9
    • 0030595366 scopus 로고    scopus 로고
    • Multiple sequence information for threading algorithms
    • Defay TR, Cohen FE. 1996. Multiple sequence information for threading algorithms. J Mol Biol 262:314-323.
    • (1996) J Mol Biol , vol.262 , pp. 314-323
    • Defay, T.R.1    Cohen, F.E.2
  • 10
    • 0030724017 scopus 로고    scopus 로고
    • Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
    • Fischer D, Eisenberg D. 1997. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 94:11929-11934.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 11929-11934
    • Fischer, D.1    Eisenberg, D.2
  • 11
    • 0029873155 scopus 로고    scopus 로고
    • Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
    • Gilis D, Rooman M. 1996. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J Mol Biol 1996:1112-1126.
    • (1996) J Mol Biol , vol.1996 , pp. 1112-1126
    • Gilis, D.1    Rooman, M.2
  • 12
    • 0029117449 scopus 로고
    • In search of the ideal protein sequence
    • Godzik A. 1995. In search of the ideal protein sequence. Protein Eng 8:409-416.
    • (1995) Protein Eng , vol.8 , pp. 409-416
    • Godzik, A.1
  • 13
    • 0026726481 scopus 로고
    • Topology fingerprint approach to the inverse protein folding problem
    • Godzik A, Skolnick J, Kolinski A. 1992. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 227:227-238.
    • (1992) J Mol Biol , vol.227 , pp. 227-238
    • Godzik, A.1    Skolnick, J.2    Kolinski, A.3
  • 14
    • 0025008445 scopus 로고
    • Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
    • Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. 1990. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol 216:167-180.
    • (1990) J Mol Biol , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floeckner, H.4    Froschauer, R.5    Gottsbacher, K.6    Casari, G.7    Sippl, M.J.8
  • 15
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C. 1993. Protein structure comparison by alignment of distance matrices. J Mol Biol 233:123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 17
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher JA, Rooman MJ, Wodak SJ. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
    • (1994) J Mol Biol , vol.235 , pp. 1598-1613
    • Kocher, J.A.1    Rooman, M.J.2    Wodak, S.J.3
  • 18
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current technologies
    • Lamer M-R, Rooman MJ, Wodak SJ. 1995. Protein structure prediction by threading methods: Evaluation of current technologies. Proteins 23:337-355.
    • (1995) Proteins , vol.23 , pp. 337-355
    • Lamer, M.-R.1    Rooman, M.J.2    Wodak, S.J.3
  • 19
    • 0031307020 scopus 로고    scopus 로고
    • Competitive assessment of protein fold recognition and alignment accuracy
    • Levitt M. 1997. Competitive assessment of protein fold recognition and alignment accuracy. Proteins suppl 1:92-104.
    • (1997) Proteins Suppl , vol.1 , pp. 92-104
    • Levitt, M.1
  • 20
    • 0028033123 scopus 로고
    • Learning about protein folding via potential functions
    • Maiorov VN, Crippen GM. 1994. Learning about protein folding via potential functions. Proteins 20:167-173.
    • (1994) Proteins , vol.20 , pp. 167-173
    • Maiorov, V.N.1    Crippen, G.M.2
  • 21
    • 0031303337 scopus 로고    scopus 로고
    • A retrospective analysis of CASP2 threading predictions
    • Marchler-Bauer A, Levitt M, Bryant SH. 1997. A retrospective analysis of CASP2 threading predictions. Proteins suppl 1:83-91.
    • (1997) Proteins Suppl , vol.1 , pp. 83-91
    • Marchler-Bauer, A.1    Levitt, M.2    Bryant, S.H.3
  • 22
    • 0029083544 scopus 로고
    • Detection of 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions
    • Matsuo Y, Nakamura H, Nishikawa K. 1995. Detection of 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions. J Biochem (Tokyo) 118:137-148.
    • (1995) J Biochem (Tokyo) , vol.118 , pp. 137-148
    • Matsuo, Y.1    Nakamura, H.2    Nishikawa, K.3
  • 23
    • 0028579433 scopus 로고
    • Protein structural similarities predicted by a sequence-structure compatibility method
    • Matsuo Y, Nishikawa K. 1994. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci 3:2055-2063.
    • (1994) Protein Sci , vol.3 , pp. 2055-2063
    • Matsuo, Y.1    Nishikawa, K.2
  • 24
    • 0028075953 scopus 로고
    • Protein stability for single substitution mutants and the extent of local compactness in the denatured state
    • Miyazawa S, Jernigan RL. 1994. Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Eng 7:1209-1220.
    • (1994) Protein Eng , vol.7 , pp. 1209-1220
    • Miyazawa, S.1    Jernigan, R.L.2
  • 25
    • 0028961335 scopus 로고
    • Scop: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. Scop: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 26
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48-443-453.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 27
    • 0027504808 scopus 로고
    • Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
    • Nishikawa K, Matsuo Y. 1993. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng 6:811-820.
    • (1993) Protein Eng , vol.6 , pp. 811-820
    • Nishikawa, K.1    Matsuo, Y.2
  • 28
    • 0029003770 scopus 로고
    • Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H
    • Ota M, Kanaya S, Nishikawa K. 1995. Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H. J Mol Biol 248:733-738.
    • (1995) J Mol Biol , vol.248 , pp. 733-738
    • Ota, M.1    Kanaya, S.2    Nishikawa, K.3
  • 29
    • 0030904226 scopus 로고    scopus 로고
    • Assessment of the pseudo-energy potential by the best-five test: A new use of the three-dimensional profiles of proteins
    • Ota M, Nishikawa K. 1997. Assessment of the pseudo-energy potential by the best-five test: A new use of the three-dimensional profiles of proteins. Protein Eng 10:339-351.
    • (1997) Protein Eng , vol.10 , pp. 339-351
    • Ota, M.1    Nishikawa, K.2
  • 30
    • 0027302043 scopus 로고
    • Prediction of protein structure by evaluation of sequence-structure fitness: Aligning sequences to contact profiles derived from 3D structures
    • Ouzounis C, Sander C, Scharf M, Schneider RJ. 1993. Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from 3D structures. J Mol Biol 232:805-825.
    • (1993) J Mol Biol , vol.232 , pp. 805-825
    • Ouzounis, C.1    Sander, C.2    Scharf, M.3    Schneider, R.J.4
  • 31
    • 0029563695 scopus 로고
    • Are database-derived potentials valid for scoring both forward and inverted protein folding?
    • Rooman MJ, Wodak SJ. 1995. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng 8:849-858.
    • (1995) Protein Eng , vol.8 , pp. 849-858
    • Rooman, M.J.1    Wodak, S.J.2
  • 32
    • 0031844330 scopus 로고    scopus 로고
    • Fold and function predictions for Mycoplasma genitalium proteins
    • Rychlewski L, Zhang B, Godzik A. 1998. Fold and function predictions for Mycoplasma genitalium proteins. Folding Design 3:229-238.
    • (1998) Folding Design , vol.3 , pp. 229-238
    • Rychlewski, L.1    Zhang, B.2    Godzik, A.3
  • 33
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. 1990. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 34
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 35
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor WR, Orengo CA. 1989. Protein structure alignment. J Mol Biol 208: 1-22.
    • (1989) J Mol Biol , vol.208 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 37
    • 0027458885 scopus 로고
    • Three-dimensional profiles from residue-pair preferences: Identification of sequences with β/α-barrel fold
    • Wilmanns M, Eisenberg D. 1993. Three-dimensional profiles from residue-pair preferences: Identification of sequences with β/α-barrel fold. Proc Natl Acad Sci USA 90:1379-1383.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 1379-1383
    • Wilmanns, M.1    Eisenberg, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.