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Volumn 7, Issue 3, 1997, Pages 377-387

Progress in protein structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 0030928268     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80055-3     Document Type: Article
Times cited : (96)

References (89)
  • 1
    • 0031025430 scopus 로고    scopus 로고
    • Into the black of night
    • A brief, but informative 'news and views' style account of the CASP2 meeting. of special interest
    • Eisenberg D. Into the black of night. Nat Struct Biol. 4:1997;95-97 A brief, but informative 'news and views' style account of the CASP2 meeting. of special interest.
    • (1997) Nat Struct Biol , vol.4 , pp. 95-97
    • Eisenberg, D.1
  • 2
    • 0031105629 scopus 로고    scopus 로고
    • Folding proteins by pattern recognition
    • Another news and views style account of CASP2, this time emphasizing the importance of pattern-recognition methods in structure prediction. of special interest
    • Shortle D. Folding proteins by pattern recognition. Curr Biol. 7:1997;R151-R154 Another news and views style account of CASP2, this time emphasizing the importance of pattern-recognition methods in structure prediction. of special interest.
    • (1997) Curr Biol , vol.7
    • Shortle, D.1
  • 3
    • 0029176077 scopus 로고
    • Protein structure prediction: A special issue
    • E.E. Lattman.
    • Lattman EE. Protein structure prediction: a special issue. Proteins. 23:1995;295-460.
    • (1995) Proteins , vol.23 , pp. 295-460
  • 4
    • 0028864205 scopus 로고
    • A critical assessment of comparative molecular modeling of tertiary structures of proteins
    • Mosimann S, Meleshko R, James MNG. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins. 23:1995;301-317.
    • (1995) Proteins , vol.23 , pp. 301-317
    • Mosimann, S.1    Meleshko, R.2    James, M.N.G.3
  • 5
    • 0030053370 scopus 로고    scopus 로고
    • PROMOD and SWISS-MODEL - Internet-based tools for automated comparative protein modeling
    • Peitsch MC. PROMOD and SWISS-MODEL - Internet-based tools for automated comparative protein modeling. Biochem Soc Trans. 24:1996;274-279.
    • (1996) Biochem Soc Trans , vol.24 , pp. 274-279
    • Peitsch, M.C.1
  • 6
    • 0026418178 scopus 로고
    • A search for the most stable folds of protein chains
    • Finkelstein AV, Reva B. A search for the most stable folds of protein chains. Nature. 351:1991;497-499.
    • (1991) Nature , vol.351 , pp. 497-499
    • Finkelstein, A.V.1    Reva, B.2
  • 7
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Lüthy, R.2    Eisenberg, D.3
  • 8
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature. 358:1992;86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 9
    • 0027050011 scopus 로고
    • Sequence-structure matching in globular proteins: Application to supersecondary and tertiary structure determination
    • Godzik A, Skolnick J. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci USA. 89:1992;12098-12102.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 12098-12102
    • Godzik, A.1    Skolnick, J.2
  • 10
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein-sequence through the folding motif
    • Bryant SH, Lawrence CE. An empirical energy function for threading protein-sequence through the folding motif. Proteins. 16:1993;92-112.
    • (1993) Proteins , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 11
    • 0027302043 scopus 로고
    • Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures
    • Ouzounis C, Sander C, Scharf M, Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J Mol Biol. 232:1993;805-825.
    • (1993) J Mol Biol , vol.232 , pp. 805-825
    • Ouzounis, C.1    Sander, C.2    Scharf, M.3    Schneider, R.4
  • 12
    • 0028304890 scopus 로고
    • Recognition of distantly related proteins through energy calculations
    • Abagyan R, Frishman D, Argos P. Recognition of distantly related proteins through energy calculations. Proteins. 19:1994;132-140.
    • (1994) Proteins , vol.19 , pp. 132-140
    • Abagyan, R.1    Frishman, D.2    Argos, P.3
  • 13
    • 0027504808 scopus 로고
    • Development of pseudoenergy potentials for assessing protein 3-D - 1-D compatibility and detecting weak homologies
    • Nishikawa K, Matsuo Y. Development of pseudoenergy potentials for assessing protein 3-D - 1-D compatibility and detecting weak homologies. Protein Eng. 6:1994;811-820.
    • (1994) Protein Eng , vol.6 , pp. 811-820
    • Nishikawa, K.1    Matsuo, Y.2
  • 16
    • 0029912991 scopus 로고    scopus 로고
    • Global optimum protein threading with gapped alignment and empirical pair score functions
    • A comprehensive paper that examines the computational complexity of the threading problem and proposes an elegant branch-and-bound search algorithm to solve it under the appropriate circumstances. One limitation of this approach is that it requires the number of secondary structures in the template structure to be fixed beforehand. This may be too limiting a restriction when applied to real threading cases. of special interest
    • Lathrop RH, Smith TF. Global optimum protein threading with gapped alignment and empirical pair score functions. J Mol Biol. 255:1996;641-665 A comprehensive paper that examines the computational complexity of the threading problem and proposes an elegant branch-and-bound search algorithm to solve it under the appropriate circumstances. One limitation of this approach is that it requires the number of secondary structures in the template structure to be fixed beforehand. This may be too limiting a restriction when applied to real threading cases. of special interest.
    • (1996) J Mol Biol , vol.255 , pp. 641-665
    • Lathrop, R.H.1    Smith, T.F.2
  • 17
    • 0028838717 scopus 로고
    • Threading a database of protein cores
    • Madej T, Gilbrat J-F, Bryant SH. Threading a database of protein cores. Proteins. 23:1995;356-369.
    • (1995) Proteins , vol.23 , pp. 356-369
    • Madej, T.1    Gilbrat, J.-F.2    Bryant, S.H.3
  • 18
    • 0028874810 scopus 로고
    • Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials
    • Hubbard TJ, Park J. Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials. Proteins. 23:1995;398-402.
    • (1995) Proteins , vol.23 , pp. 398-402
    • Hubbard, T.J.1    Park, J.2
  • 19
    • 0029996682 scopus 로고    scopus 로고
    • Search for the most stable folds of protein chains. 1. Application of a self-consistent molecular field theory to a problem of protein 3-dimensional structure prediction
    • See annotation [20]. of special interest
    • Reva A, Finkelstein AV. Search for the most stable folds of protein chains. 1. Application of a self-consistent molecular field theory to a problem of protein 3-dimensional structure prediction. Protein Eng. 9:1996;387-397 See annotation [20]. of special interest.
    • (1996) Protein Eng , vol.9 , pp. 387-397
    • Reva, A.1    Finkelstein, A.V.2
  • 20
    • 0030006836 scopus 로고    scopus 로고
    • Search for the most stable folds of protein chains. 2. Computation of stable architectures of beta-proteins using a self-consistent molecular-field theory
    • These two papers [19,20] describe the latest work by Reva and Finkelstein on their mean-field approach to threading, which really can be thought of as the archetypal threading method - it even predates the inception of the word threading itself. Their approach helps explain why threading can work when specific contacts are not preserved between structurally similar but nonhomologous protein structures. However, the use of a lattice representation, which is necessary to allow the mean-field to be calculated, is really too restrictive; although, as these papers show, the authors are trying to work around this. of special interest
    • Reva A, Finkelstein AV. Search for the most stable folds of protein chains. 2. Computation of stable architectures of beta-proteins using a self-consistent molecular-field theory. Protein Eng. 9:1996;399-411 These two papers [19,20] describe the latest work by Reva and Finkelstein on their mean-field approach to threading, which really can be thought of as the archetypal threading method - it even predates the inception of the word threading itself. Their approach helps explain why threading can work when specific contacts are not preserved between structurally similar but nonhomologous protein structures. However, the use of a lattice representation, which is necessary to allow the mean-field to be calculated, is really too restrictive; although, as these papers show, the authors are trying to work around this. of special interest.
    • (1996) Protein Eng , vol.9 , pp. 399-411
    • Reva, A.1    Finkelstein, A.V.2
  • 21
    • 0029874551 scopus 로고    scopus 로고
    • Protein fold recognition using sequence-derived predictions
    • The latest incarnation of the work that started out as the 1D - 3D profile method (inverse protein folding) has progressed now towards a more general fold-recognition method. In this paper predicted secondary-structure features are used in the matching algorithm, and this combination seems to perform well in the CASP2 tests. of special interest
    • Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955 The latest incarnation of the work that started out as the 1D - 3D profile method (inverse protein folding) has progressed now towards a more general fold-recognition method. In this paper predicted secondary-structure features are used in the matching algorithm, and this combination seems to perform well in the CASP2 tests. of special interest.
    • (1996) Protein Sci , vol.5 , pp. 947-955
    • Fischer, D.1    Eisenberg, D.2
  • 22
    • 0030595366 scopus 로고    scopus 로고
    • Multiple sequence information for threading algorithms
    • Many groups have considered that information from multiple sequence alignments should help improve the accuracy and sensitivity of fold recognition. This is the first example of a working implementation of these ideas. The results seem to be very impressive when compared with single-sequence threading methods, but the method was not included in the CASP2 assessment and so how well it will perform under blind-testing is still not clear. of special interest
    • Defay TR, Cohen FE. Multiple sequence information for threading algorithms. J Mol Biol. 262:1996;314-323 Many groups have considered that information from multiple sequence alignments should help improve the accuracy and sensitivity of fold recognition. This is the first example of a working implementation of these ideas. The results seem to be very impressive when compared with single-sequence threading methods, but the method was not included in the CASP2 assessment and so how well it will perform under blind-testing is still not clear. of special interest.
    • (1996) J Mol Biol , vol.262 , pp. 314-323
    • Defay, T.R.1    Cohen, F.E.2
  • 23
    • 0029951995 scopus 로고    scopus 로고
    • Protein fold recognition by mapping predicted secondary structures
    • A nicely presented account of an alternative approach to fold recognition whereby predicted secondary structures are mapped onto the secondary structural regions in a library of folds. The results presented here are very impressive, although the secondary-structure predictions used in the examples appear to be of better than average quality, and how well this kind of approach will fare when given rather poor secondary structure prediction data as input is not clear. Nevertheless, this approach will be extremely useful in cases where there are many homologous sequences available with which to make an accurate prediction of secondary structure. of special interest
    • Russell RB, Copley RR, Barton GJ. Protein fold recognition by mapping predicted secondary structures. J Mol Biol. 259:1996;349-365 A nicely presented account of an alternative approach to fold recognition whereby predicted secondary structures are mapped onto the secondary structural regions in a library of folds. The results presented here are very impressive, although the secondary-structure predictions used in the examples appear to be of better than average quality, and how well this kind of approach will fare when given rather poor secondary structure prediction data as input is not clear. Nevertheless, this approach will be extremely useful in cases where there are many homologous sequences available with which to make an accurate prediction of secondary structure. of special interest.
    • (1996) J Mol Biol , vol.259 , pp. 349-365
    • Russell, R.B.1    Copley, R.R.2    Barton, G.J.3
  • 24
    • 0029974002 scopus 로고    scopus 로고
    • Evaluation of threading specificity and accuracy
    • This paper examines the problem of alignment accuracy in threading and attempts to investigate under what circumstances an accurate alignment from threading can be expected. This kind of investigation is important as, despite the apparently good alignments submitted to CASP2 in the threading section, lack of alignment accuracy is still a major problem for threading methods. of special interest
    • Bryant SH. Evaluation of threading specificity and accuracy. Proteins. 26:1996;172-185 This paper examines the problem of alignment accuracy in threading and attempts to investigate under what circumstances an accurate alignment from threading can be expected. This kind of investigation is important as, despite the apparently good alignments submitted to CASP2 in the threading section, lack of alignment accuracy is still a major problem for threading methods. of special interest.
    • (1996) Proteins , vol.26 , pp. 172-185
    • Bryant, S.H.1
  • 25
  • 26
    • 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, Floackner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. 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. 216:1990;167-180.
    • (1990) J Mol Biol , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floackner, H.4    Froschauer, R.5    Gottsbacher, K.6    Casari, G.7    Sippl, M.J.8
  • 27
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol. 227:1992;876-888.
    • (1992) J Mol Biol , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 28
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence - structure matches
    • Kocher JPA, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence - structure matches. J Mol Biol. 235:1994;1598-1613.
    • (1994) J Mol Biol , vol.235 , pp. 1598-1613
    • Kocher, J.P.A.1    Rooman, M.J.2    Wodak, S.J.3
  • 29
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • Park BH, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol. 266:1997;831-846.
    • (1997) J Mol Biol , vol.266 , pp. 831-846
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 30
    • 0029919190 scopus 로고    scopus 로고
    • Residue - residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S, Jernigan RL. Residue - residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol. 256:1996;623-644.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 31
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • A simple yet apparently effective method is proposed for optimizing the parameters in a pair-potential function such that the native folds for a given set of protein sequences are maximally discriminated from decoy conformations. of outstanding interest
    • Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci USA. 93:1996;11628-11633 A simple yet apparently effective method is proposed for optimizing the parameters in a pair-potential function such that the native folds for a given set of protein sequences are maximally discriminated from decoy conformations. of outstanding interest.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 32
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park B, Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J Mol Biol. 258:1996;367-392.
    • (1996) J Mol Biol , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 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. 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. 213:1990;859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 34
    • 0028801308 scopus 로고
    • Why do protein architectures have Boltzmann-like statistics?
    • Finkelstein AV, Badretdinov AY, Gutin AM. Why do protein architectures have Boltzmann-like statistics? Proteins. 23:1995;142-150.
    • (1995) Proteins , vol.23 , pp. 142-150
    • Finkelstein, A.V.1    Badretdinov, A.Y.2    Gutin, A.M.3
  • 35
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures - how accurate are they?
    • Thomas PD, Dill KA. Statistical potentials extracted from protein structures - how accurate are they? J Mol Biol. 257:1996;457-469.
    • (1996) J Mol Biol , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 36
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? A new approach to an old problem
    • Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol. 264:1996;1164-1179.
    • (1996) J Mol Biol , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 37
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current techniques
    • Lemer CMR, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. Proteins. 23:1995;337-355.
    • (1995) Proteins , vol.23 , pp. 337-355
    • Lemer, C.M.R.1    Rooman, M.J.2    Wodak, S.J.3
  • 38
  • 39
    • 0028306109 scopus 로고
    • Crystal structure of CspA, the major cold shock protein of Escherichia coli
    • Schindelin H, Jiang W, Inouye M, Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc Natl Acad Sci USA. 91:1994;5119-5123.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 5119-5123
    • Schindelin, H.1    Jiang, W.2    Inouye, M.3    Heinemann, U.4
  • 41
    • 0029922311 scopus 로고    scopus 로고
    • Xylanase homology modeling using the inverse protein folding approach
    • Chen X, Whitmire D, Bowen JP. Xylanase homology modeling using the inverse protein folding approach. Protein Sci. 5:1996;705-708.
    • (1996) Protein Sci , vol.5 , pp. 705-708
    • Chen, X.1    Whitmire, D.2    Bowen, J.P.3
  • 42
    • 0030052366 scopus 로고    scopus 로고
    • Protein fold recognition by sequence threading - tools and assessment techniques
    • Miller RT, Jones DT, Thornton JM. Protein fold recognition by sequence threading - tools and assessment techniques. FASEB J. 10:1996;171-178.
    • (1996) FASEB J , vol.10 , pp. 171-178
    • Miller, R.T.1    Jones, D.T.2    Thornton, J.M.3
  • 43
    • 0030581168 scopus 로고    scopus 로고
    • Assessment of protein fold predictions from sequence information: The predicted alpha/beta doubly wound fold of the von Willebrand factor type a domain is similar to its crystal structure
    • This paper describes the results of an attempt to predict the structure of a protein before the structure is known. What makes this paper particularly impressive is not just the accuracy of the resulting prediction, but the fact that the authors are not specialists in the prediction field. Hopefully, many more experimentalists will follow suit and start making use of the available prediction tools. A novel method for enhancing the accuracy of fold recognition is described whereby individual threading results are averaged across a family of sequences. of outstanding interest
    • Edwards YJK, Perkins SJ. Assessment of protein fold predictions from sequence information: the predicted alpha/beta doubly wound fold of the von Willebrand factor type a domain is similar to its crystal structure. J Mol Biol. 260:1996;277-285 This paper describes the results of an attempt to predict the structure of a protein before the structure is known. What makes this paper particularly impressive is not just the accuracy of the resulting prediction, but the fact that the authors are not specialists in the prediction field. Hopefully, many more experimentalists will follow suit and start making use of the available prediction tools. A novel method for enhancing the accuracy of fold recognition is described whereby individual threading results are averaged across a family of sequences. of outstanding interest.
    • (1996) J Mol Biol , vol.260 , pp. 277-285
    • Edwards, Y.J.K.1    Perkins, S.J.2
  • 44
    • 0022631926 scopus 로고
    • The folding type of a protein is relevant to the amino acid composition
    • Nakashima H, Nishikawa K, Ooi T. The folding type of a protein is relevant to the amino acid composition. J Biochem. 99:1986;153-162.
    • (1986) J Biochem , vol.99 , pp. 153-162
    • Nakashima, H.1    Nishikawa, K.2    Ooi, T.3
  • 45
    • 0029946575 scopus 로고    scopus 로고
    • Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods
    • See annotation [46]. of outstanding interest
    • Eisenhaber F, Frommel C, Argos P. Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods. Proteins. 25:1996;157-168 See annotation [46]. of outstanding interest.
    • (1996) Proteins , vol.25 , pp. 157-168
    • Eisenhaber, F.1    Frommel, C.2    Argos, P.3
  • 46
    • 0029902174 scopus 로고    scopus 로고
    • Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class
    • These two papers [45,46] contain an excellent, thorough analysis of how much information about the secondary-structure content can be extracted from amino acid composition. Many of the conclusions reached by the authors can be applied to many other areas of structure prediction. of outstanding interest
    • Eisenhaber F, Frommel C, Argos P. Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class. Proteins. 25:1996;169-179 These two papers [45,46] contain an excellent, thorough analysis of how much information about the secondary-structure content can be extracted from amino acid composition. Many of the conclusions reached by the authors can be applied to many other areas of structure prediction. of outstanding interest.
    • (1996) Proteins , vol.25 , pp. 169-179
    • Eisenhaber, F.1    Frommel, C.2    Argos, P.3
  • 47
    • 0027997161 scopus 로고
    • The DEF data base of sequence based protein fold class predictions
    • Reczko M, Bohr H. The DEF data base of sequence based protein fold class predictions. Nucleic Acids Res. 22:1994;3616-3619.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3616-3619
    • Reczko, M.1    Bohr, H.2
  • 48
    • 0029149907 scopus 로고
    • Protein secondary structure prediction
    • Barton GJ. Protein secondary structure prediction. Curr Opin Struct Biol. 5:1995;372-376.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 372-376
    • Barton, G.J.1
  • 49
    • 0028783819 scopus 로고
    • Progress of 1D protein structure prediction at last
    • Rost B, Sander C. Progress of 1D protein structure prediction at last. Proteins. 23:1995;295-300.
    • (1995) Proteins , vol.23 , pp. 295-300
    • Rost, B.1    Sander, C.2
  • 50
    • 0031022743 scopus 로고    scopus 로고
    • Improvement of protein secondary structure prediction using binary word encoding
    • Kawabata T, Doi J. Improvement of protein secondary structure prediction using binary word encoding. Proteins. 27:1997;36-46.
    • (1997) Proteins , vol.27 , pp. 36-46
    • Kawabata, T.1    Doi, J.2
  • 51
    • 0029804192 scopus 로고    scopus 로고
    • Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
    • A simple, yet apparently effective approach to secondary-structure prediction. This bucks the recent trend for secondary-structure prediction methods to be extremely complex. The program code that implements the method is freely available from the authors. of outstanding interest
    • King RD, Sternberg MJE. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci. 5:1996;2298-2310 A simple, yet apparently effective approach to secondary-structure prediction. This bucks the recent trend for secondary-structure prediction methods to be extremely complex. The program code that implements the method is freely available from the authors. of outstanding interest.
    • (1996) Protein Sci , vol.5 , pp. 2298-2310
    • King, R.D.1    Sternberg, M.J.E.2
  • 52
    • 0030601801 scopus 로고    scopus 로고
    • Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses
    • This method should not be taken as a competitor in the 'best secondary structure prediction method' stakes. The main aim of this paper is to demonstrate a simple way of extracting evolutionary information from multiply aligned sequences such that the evolutionary information remains faithful to a good evolutionary tree. Simpler methods for exploiting the information from multiple sequence alignments, such as constructing simple averaged profiles, are shown to lose a substantial degree of information, and biases in the choice of sequences are seen to hamper prediction accuracy unless an explicit evolutionary tree is calculated. These results can be applied to any prediction method based on multiply aligned sequences. of special interest
    • Goldman N, Thorne JL, Jones DT. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol. 263:1996;196-208 This method should not be taken as a competitor in the 'best secondary structure prediction method' stakes. The main aim of this paper is to demonstrate a simple way of extracting evolutionary information from multiply aligned sequences such that the evolutionary information remains faithful to a good evolutionary tree. Simpler methods for exploiting the information from multiple sequence alignments, such as constructing simple averaged profiles, are shown to lose a substantial degree of information, and biases in the choice of sequences are seen to hamper prediction accuracy unless an explicit evolutionary tree is calculated. These results can be applied to any prediction method based on multiply aligned sequences. of special interest.
    • (1996) J Mol Biol , vol.263 , pp. 196-208
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 53
    • 0030581145 scopus 로고    scopus 로고
    • The use of amino acid patterns of classified helices and strands in secondary structure prediction
    • Zhu ZY, Blundell TL. The use of amino acid patterns of classified helices and strands in secondary structure prediction. J Mol Biol. 260:1996;261-276.
    • (1996) J Mol Biol , vol.260 , pp. 261-276
    • Zhu, Z.Y.1    Blundell, T.L.2
  • 54
    • 0029884694 scopus 로고    scopus 로고
    • GOR method for predicting protein secondary structure from amino acid sequence
    • Garnier J, Gibrat JF, Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266:1996;540-553.
    • (1996) Methods Enzymol , vol.266 , pp. 540-553
    • Garnier, J.1    Gibrat, J.F.2    Robson, B.3
  • 55
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 18:1994;309-317.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Gobel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 56
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    • Shindyalov IN, Kolchanov NA, Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7:1994;349-358.
    • (1994) Protein Eng , vol.7 , pp. 349-358
    • Shindyalov, I.N.1    Kolchanov, N.A.2    Sander, C.3
  • 57
    • 0027952860 scopus 로고
    • Compensating changes in protein multiple sequence alignments
    • Taylor WR, Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng. 7:1994;341-348.
    • (1994) Protein Eng , vol.7 , pp. 341-348
    • Taylor, W.R.1    Hatrick, K.2
  • 58
    • 0029850738 scopus 로고    scopus 로고
    • The prediction of protein contacts from multiple sequence alignments
    • Thomas DJ, Casari G, Sander C. The prediction of protein contacts from multiple sequence alignments. Protein Eng. 9:1996;941-948.
    • (1996) Protein Eng , vol.9 , pp. 941-948
    • Thomas, D.J.1    Casari, G.2    Sander, C.3
  • 59
    • 0028326042 scopus 로고
    • Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
    • Kolinski A, Skolnick J. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. Proteins. 18:1994;353-366.
    • (1994) Proteins , vol.18 , pp. 353-366
    • Kolinski, A.1    Skolnick, J.2
  • 60
    • 0028049306 scopus 로고
    • Lattice model simulations of polypeptide chain folding
    • Covell DG. Lattice model simulations of polypeptide chain folding. J Mol Biol. 235:1994;1032-1043.
    • (1994) J Mol Biol , vol.235 , pp. 1032-1043
    • Covell, D.G.1
  • 61
    • 0028175436 scopus 로고
    • A method for alpha-helical integral membrane protein fold prediction
    • Taylor WR, Jones DT, Green NM. A method for alpha-helical integral membrane protein fold prediction. Proteins. 18:1994;281-294.
    • (1994) Proteins , vol.18 , pp. 281-294
    • Taylor, W.R.1    Jones, D.T.2    Green, N.M.3
  • 62
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • Kolinski A, Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins. 18:1994;338-352.
    • (1994) Proteins , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 63
    • 0028124611 scopus 로고
    • Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry
    • Yee DP, Chan HS, Havel TF, Dill KA. Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry. J Mol Biol. 241:1994;557-573.
    • (1994) J Mol Biol , vol.241 , pp. 557-573
    • Yee, D.P.1    Chan, H.S.2    Havel, T.F.3    Dill, K.A.4
  • 64
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol. 243:1994;668-682.
    • (1994) J Mol Biol , vol.243 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 67
    • 0029063717 scopus 로고
    • The complexity and accuracy of discrete state models of protein structure
    • Park BH, Levitt M. The complexity and accuracy of discrete state models of protein structure. J Mol Biol. 249:1995;493-507.
    • (1995) J Mol Biol , vol.249 , pp. 493-507
    • Park, B.H.1    Levitt, M.2
  • 69
    • 0029016005 scopus 로고
    • Accurate general method for lattice approximation of three-dimensional structure of a chain molecule
    • Rykunov DS, Reva BA, Finkelstein AV. Accurate general method for lattice approximation of three-dimensional structure of a chain molecule. Proteins. 22:1995;100-109.
    • (1995) Proteins , vol.22 , pp. 100-109
    • Rykunov, D.S.1    Reva, B.A.2    Finkelstein, A.V.3
  • 70
    • 0029079963 scopus 로고
    • Exhaustive enumeration of protein conformations using experimental restraints
    • Dewitte RS, Michnick SW, Shakhnovich EI. Exhaustive enumeration of protein conformations using experimental restraints. Protein Sci. 4:1995;1780-1791.
    • (1995) Protein Sci , vol.4 , pp. 1780-1791
    • Dewitte, R.S.1    Michnick, S.W.2    Shakhnovich, E.I.3
  • 72
    • 0029987096 scopus 로고    scopus 로고
    • Does a backwardly read protein sequence have a unique native state?
    • Given the lack of success that is evident in folding sequences in the normal direction, it is perhaps a little premature to be asking this kind of question. Despite this, however, this paper does a good job of addressing the question at hand, and it is undoubtedly thought provoking. of special interest
    • Olszewski KA, Kolinski A, Skolnick J. Does a backwardly read protein sequence have a unique native state? Protein Eng. 9:1996;5-14 Given the lack of success that is evident in folding sequences in the normal direction, it is perhaps a little premature to be asking this kind of question. Despite this, however, this paper does a good job of addressing the question at hand, and it is undoubtedly thought provoking. of special interest.
    • (1996) Protein Eng , vol.9 , pp. 5-14
    • Olszewski, K.A.1    Kolinski, A.2    Skolnick, J.3
  • 73
    • 0030018099 scopus 로고    scopus 로고
    • Folding simulations and computer redesign of protein A three-helix bundle motifs
    • Olszewski KA, Kolinski A, Skolnick J. Folding simulations and computer redesign of protein A three-helix bundle motifs. Proteins. 25:1996;286-299.
    • (1996) Proteins , vol.25 , pp. 286-299
    • Olszewski, K.A.1    Kolinski, A.2    Skolnick, J.3
  • 74
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li H, Helling R, Tang C, Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science. 273:1996;666-669.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 75
    • 0029786785 scopus 로고    scopus 로고
    • Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator
    • Rabow AA, Scheraga HA. Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator. Protein Sci. 5:1996;1800-1815.
    • (1996) Protein Sci , vol.5 , pp. 1800-1815
    • Rabow, A.A.1    Scheraga, H.A.2
  • 76
    • 0029797368 scopus 로고    scopus 로고
    • Building self-avoiding lattice models of proteins using a self-consistent field optimization
    • Reva BA, Finkelstein AV, Rykunov DS, Olson AJ. Building self-avoiding lattice models of proteins using a self-consistent field optimization. Proteins. 26:1996;1-8.
    • (1996) Proteins , vol.26 , pp. 1-8
    • Reva, B.A.1    Finkelstein, A.V.2    Rykunov, D.S.3    Olson, A.J.4
  • 77
    • 0029909775 scopus 로고    scopus 로고
    • A fast conformational search strategy for finding low energy structures of model proteins
    • Beutler TC, Dill KA. A fast conformational search strategy for finding low energy structures of model proteins. Protein Sci. 5:1996;2037-2043.
    • (1996) Protein Sci , vol.5 , pp. 2037-2043
    • Beutler, T.C.1    Dill, K.A.2
  • 78
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • Methods that can take a variety of weak structural constraints such as predicted secondary structure, predicted contacts or known disulphide connectivity are likely to be very powerful tools, not only for structure prediction, but also for structure determination (NMR spectroscopy in particular) as well. of special interest
    • Skolnick J, Kolinski A, Ortiz AR. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol. 265:1997;217-241 Methods that can take a variety of weak structural constraints such as predicted secondary structure, predicted contacts or known disulphide connectivity are likely to be very powerful tools, not only for structure prediction, but also for structure determination (NMR spectroscopy in particular) as well. of special interest.
    • (1997) J Mol Biol , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 79
    • 0028297304 scopus 로고
    • Folding the main chain of small proteins with the genetic algorithm
    • Dandekar T, Argos P. Folding the main chain of small proteins with the genetic algorithm. J Mol Biol. 236:1994;844-861.
    • (1994) J Mol Biol , vol.236 , pp. 844-861
    • Dandekar, T.1    Argos, P.2
  • 80
    • 0029132872 scopus 로고
    • A genetic algorithm that seeks native states of peptides and proteins
    • Sun S. A genetic algorithm that seeks native states of peptides and proteins. Biophys J. 69:1995;340-355.
    • (1995) Biophys J , vol.69 , pp. 340-355
    • Sun, S.1
  • 81
    • 0029085037 scopus 로고
    • Local moves: An efficient algorithm for simulation of protein folding
    • Elofsson A, Le Grand SM, Eisenberg D. Local moves: an efficient algorithm for simulation of protein folding. Proteins. 23:1995;73-82.
    • (1995) Proteins , vol.23 , pp. 73-82
    • Elofsson, A.1    Le Grand, S.M.2    Eisenberg, D.3
  • 82
    • 0028841399 scopus 로고
    • A simple protein folding algorithm using a binary code and secondary structure constraints
    • Sun S, Thomas PD, Dill KA. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8:1995;769-778.
    • (1995) Protein Eng , vol.8 , pp. 769-778
    • Sun, S.1    Thomas, P.D.2    Dill, K.A.3
  • 83
    • 0029055313 scopus 로고
    • LINUS - A hierarchical procedure to predict the fold of a protein
    • Srinivasan R, Rose GD. LINUS - a hierarchical procedure to predict the fold of a protein. Proteins. 22:1995;81-99.
    • (1995) Proteins , vol.22 , pp. 81-99
    • Srinivasan, R.1    Rose, G.D.2
  • 84
    • 0028865590 scopus 로고
    • Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms
    • Pederson JT, Moult J. Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins. 23:1995;454-460.
    • (1995) Proteins , vol.23 , pp. 454-460
    • Pederson, J.T.1    Moult, J.2
  • 85
    • 0030051017 scopus 로고    scopus 로고
    • Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm
    • Dandekar T, Argos P. Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm. Int J Biol Macromol. 18:1996;1-4.
    • (1996) Int J Biol Macromol , vol.18 , pp. 1-4
    • Dandekar, T.1    Argos, P.2
  • 86
    • 0029984690 scopus 로고    scopus 로고
    • Genetic algorithms for protein structure prediction
    • A good review of the use of genetic algorithms in different methods used in the protein folding field. Most people now seem to be convinced of the power of genetic algorithms. The fact that conformational space is searched in parallel by many individuals in the population seems to be the key feature that makes genetic algorithms so powerful for protein folding studies. of special interest
    • Pedersen JT, Moult J. Genetic algorithms for protein structure prediction. Curr Opin Struct Biol. 6:1996;227-231 A good review of the use of genetic algorithms in different methods used in the protein folding field. Most people now seem to be convinced of the power of genetic algorithms. The fact that conformational space is searched in parallel by many individuals in the population seems to be the key feature that makes genetic algorithms so powerful for protein folding studies. of special interest.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 227-231
    • Pedersen, J.T.1    Moult, J.2
  • 87
    • 0029888335 scopus 로고    scopus 로고
    • Polypeptide folding with-off lattice Monte Carlo dynamics: The method
    • Hoffmann D, Knapp EW. Polypeptide folding with-off lattice Monte Carlo dynamics: the method. Eur Biophys J. 24:1996;387-403.
    • (1996) Eur Biophys J , vol.24 , pp. 387-403
    • Hoffmann, D.1    Knapp, E.W.2
  • 88
    • 0030322828 scopus 로고    scopus 로고
    • Homology modelling by distance geometry
    • This paper is a latest in a series that describes the various incarnations of the DRAGON program - a very flexible method for calculating simplified protein chain conformations based on distance geometry. In this paper, the method is applied to the problem of homology modelling, but, in previous papers, the method has been applied to the construction of stereochemically plausible conformations that satisfy a small number of geometric constraints. It has not yet been applied to the problem of completely ab initio protein structure prediction. This kind of approach is not really suitable for modelling closely related protein structures, as too much useful information is ignored (the maximum inheritance principle - see text). This method is very fast, however, and may well be very useful when combined with a threading method. of special interest
    • Aszodi A, Taylor WR. Homology modelling by distance geometry. Fold Des. 1:1996;325-334 This paper is a latest in a series that describes the various incarnations of the DRAGON program - a very flexible method for calculating simplified protein chain conformations based on distance geometry. In this paper, the method is applied to the problem of homology modelling, but, in previous papers, the method has been applied to the construction of stereochemically plausible conformations that satisfy a small number of geometric constraints. It has not yet been applied to the problem of completely ab initio protein structure prediction. This kind of approach is not really suitable for modelling closely related protein structures, as too much useful information is ignored (the maximum inheritance principle - see text). This method is very fast, however, and may well be very useful when combined with a threading method. of special interest.
    • (1996) Fold des , vol.1 , pp. 325-334
    • Aszodi, A.1    Taylor, W.R.2
  • 89
    • 0003047663 scopus 로고
    • Fitting 1D predictions into 3D structures
    • H. Bohr, Brunak S. Boca Raton, Florida: CRC Press
    • Rost B. Fitting 1D predictions into 3D structures. Bohr H, Brunak S. Protein Folds. A Distance Based Approach. 1995;132-151 CRC Press, Boca Raton, Florida.
    • (1995) Protein Folds. a Distance Based Approach , pp. 132-151
    • Rost, B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.