-
1
-
-
0031025430
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
15
-
-
0028802198
-
Progress in fold recognition
-
Flöckner H, Braxenthaler M, Lackner P, Jaritz M, Ortner M, Sippl MJ. Progress in fold recognition. Proteins. 23:1995;376-386.
-
(1995)
Proteins
, vol.23
, pp. 376-386
-
-
Flöckner, H.1
Braxenthaler, M.2
Lackner, P.3
Jaritz, M.4
Ortner, M.5
Sippl, M.J.6
-
16
-
-
0029912991
-
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
-
18
-
-
0028874810
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
26
-
-
0025008445
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
0029554779
-
Protein fold recognition by threading - comparison of algorithms and analysis of results
-
Westhead DR, Collura VP, Eldridge MD, Firth MA, Li J, Murray CW. Protein fold recognition by threading - comparison of algorithms and analysis of results. Protein Eng. 8:1995;1197-1204.
-
(1995)
Protein Eng
, vol.8
, pp. 1197-1204
-
-
Westhead, D.R.1
Collura, V.P.2
Eldridge, M.D.3
Firth, M.A.4
Li, J.5
Murray, C.W.6
-
39
-
-
0028306109
-
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
-
40
-
-
0025292662
-
The epidermolytic toxins are serine proteases
-
Dancer SJ, Garratt R, Saldanha J, Jhoti H, Evans R. The epidermolytic toxins are serine proteases. FEBS Lett. 268:1990;129-132.
-
(1990)
FEBS Lett
, vol.268
, pp. 129-132
-
-
Dancer, S.J.1
Garratt, R.2
Saldanha, J.3
Jhoti, H.4
Evans, R.5
-
41
-
-
0029922311
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
65
-
-
0028963219
-
A test of lattice protein folding algorithms
-
Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. A test of lattice protein folding algorithms. Proc Natl Acad Sci USA. 92:1995;325-329.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 325-329
-
-
Yue, K.1
Fiebig, K.M.2
Thomas, P.D.3
Chan, H.S.4
Shakhnovich, E.I.5
Dill, K.A.6
-
66
-
-
0028929556
-
Principles of protein folding - A perspective from simple exact models
-
Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:1995;561-602.
-
(1995)
Protein Sci
, vol.4
, pp. 561-602
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
Fiebig, K.M.4
Yee, D.P.5
Thomas, P.D.6
Chan, H.S.7
-
67
-
-
0029063717
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
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