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of special interest. J. Moult, R. Judson, K. Fidelis, & J.T. Pedersen. This is a short account of the Meeting on the Critical Assessment of Protein Structure Prediction Methods ([CASP]-1; 1994 December 4-8, Asilomar, USA) and a preface to the proceedings of the meeting that are published in the same special issue of Proteins.
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of special interest Moult J, Judson R, Fidelis K, Pedersen JT. Large scale experiment to assess protein structure prediction methods. Proteins. 23:1995;ii-iv This is a short account of the Meeting on the Critical Assessment of Protein Structure Prediction Methods ([CASP]-1; 1994 December 4-8, Asilomar, USA) and a preface to the proceedings of the meeting that are published in the same special issue of Proteins.
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of special interest. of outstanding interest. This paper contains a comprehensive analysis of the results of the Asilomar contest [11] in 'threading'. Threading is a technique that aligns a protein sequence with a set of known 3D structures to select the correct fold of this sequence from a set of alternatives. It is shown that when the native fold of the examined chain is close to some fold from the set, the threading methods can more or less often (but not always) recognize the correct fold as one of the most probable ones for this sequence. The sequence-structure alignments in all the correctly recognized folds, however, are suprisingly poor, in other words, threading cannot currently derive a detailed 3D model from the amino-acid sequence. It is suggested that the fold recognition is actually based upon recognition of only rough structural features: secondary structures and hydrophobic interactions in the protein core. The review also contains a brief but very informative
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of special interest Lemer CMR, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. of outstanding interest Proteins. 23:1995;337-355 This paper contains a comprehensive analysis of the results of the Asilomar contest [11] in 'threading'. Threading is a technique that aligns a protein sequence with a set of known 3D structures to select the correct fold of this sequence from a set of alternatives. It is shown that when the native fold of the examined chain is close to some fold from the set, the threading methods can more or less often (but not always) recognize the correct fold as one of the most probable ones for this sequence. The sequence-structure alignments in all the correctly recognized folds, however, are suprisingly poor, in other words, threading cannot currently derive a detailed 3D model from the amino-acid sequence. It is suggested that the fold recognition is actually based upon recognition of only rough structural features: secondary structures and hydrophobic interactions in the protein core. The review also contains a brief but very informative classification of threading methods.
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Proteins
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Lemer, C.M.R.1
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of special interest. The assessment shows that comparative molecular modelling is highly successful when sequence identify exceeds 70%, and is poor when the identity is below 30%. Where the sequence alignment is in error (e.g. in regions of poor local homology) the comparative model is guaranteed to be wrong. The most serious errors occur in the regions of insertions and deletions.
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Mosiman S, Melishko R, James MGN. A critical assessment of comparative molecular modelling of tertiary structure of proteins. of special interest Proteins. 23:1995;301-317 The assessment shows that comparative molecular modelling is highly successful when sequence identify exceeds 70%, and is poor when the identity is below 30%. Where the sequence alignment is in error (e.g. in regions of poor local homology) the comparative model is guaranteed to be wrong. The most serious errors occur in the regions of insertions and deletions.
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Mosiman, S.1
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of outstanding interest. This paper reviews the results of an ab initio protein-structure prediction contest from the level of secondary structure to the level of 3D folds. The results show that ab initio prediction of novel folds and, in general, an accurate tertiary-structure prediction is not yet possible. Protein fold and motif recognition are possible, however, when the motif is sufficiently similar to another, already known protein structure. The predictions are facilitated by aligned families of homologues sequences. The paper includes a very useful summary of the ab initio prediction techniques used for the Asilomar contest [11].
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Defay T, Cohen FE. Evaluation of current techniques for ab initio protein structure prediction. of outstanding interest Proteins. 23:1995;431-445 This paper reviews the results of an ab initio protein-structure prediction contest from the level of secondary structure to the level of 3D folds. The results show that ab initio prediction of novel folds and, in general, an accurate tertiary-structure prediction is not yet possible. Protein fold and motif recognition are possible, however, when the motif is sufficiently similar to another, already known protein structure. The predictions are facilitated by aligned families of homologues sequences. The paper includes a very useful summary of the ab initio prediction techniques used for the Asilomar contest [11].
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of special interest. This is an account of a practical workshop on protein-structure prediction with a very useful list of software used in the course of predictions.
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of special interest. W.F. Van Gunstren, P.K. Weinevandt, Willeinson A.J. ESCOM Science Publications, Leiden, A comprehensive review of work on Monte-Carlo lattice simulations of protein folding
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of special interest. Based on the Asilomar critical assessment [11], this paper shows that the accuracy of secondary-structure predictions has improved significantly (up to 72±9% for correctly predicting the α, β, or coil state of a residue) by using information contained in multiple sequence alignments as input to a neural network system [31].
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Rost B, Sander C. Progress of 1D protein structure prediction at last. of special interest Proteins. 23:1995;295-300 Based on the Asilomar critical assessment [11], this paper shows that the accuracy of secondary-structure predictions has improved significantly (up to 72±9% for correctly predicting the α, β, or coil state of a residue) by using information contained in multiple sequence alignments as input to a neural network system [31].
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of special interest. The paper analyzes the authors' blind predictions of protein structures. The predictions were carried out as follows: first, a secondary structure was predicted as a consensus structure from the multiple sequence alignments; and second, a tertiary structure was chosen by threading of the predicted secondary structure onto proteins of known 3D structure.
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Benner SA, Gerloff D, Chelvanayagam G. The phosphogalactosidase and synaptotagmin prediction. of special interest Proteins. 23:1995;446-453 The paper analyzes the authors' blind predictions of protein structures. The predictions were carried out as follows: first, a secondary structure was predicted as a consensus structure from the multiple sequence alignments; and second, a tertiary structure was chosen by threading of the predicted secondary structure onto proteins of known 3D structure.
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Proteins
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Benner, S.A.1
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of special interest. Blind predictions of protein structures are presented. The 'Note added in proof' compares the authors' and Bazan's [34] predictions with the subsequently resolved cyclin crystal structure. Although the secondary structure predictions (both obtained from multiple sequence alignments) are extremely good (especially Bazan's one), the predictions of tertiary structures did not turn out to be successful.
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Gerloff DL, Cohen FE. Secondary structure prediction and unrefined tertiary structure prediction for the cyclin A, B and D. of special interest Proteins. 24:1996;18-34 Blind predictions of protein structures are presented. The 'Note added in proof' compares the authors' and Bazan's [34] predictions with the subsequently resolved cyclin crystal structure. Although the secondary structure predictions (both obtained from multiple sequence alignments) are extremely good (especially Bazan's one), the predictions of tertiary structures did not turn out to be successful.
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Proteins
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of special interest. The algorithm discussed predicts the tertiary structures of small proteins from their sequences, and their secondary structures using a small number of energy parameters.
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Sun S, Thomas PD, Dill KA. A simple protein folding algorithm using a binary code and secondary structure constraints. of special interest Protein Eng. 8:1995;769-778 The algorithm discussed predicts the tertiary structures of small proteins from their sequences, and their secondary structures using a small number of energy parameters.
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of outstanding interest. This paper contains an assessment of the blind recognition of protein folds carried out by Sippl and his group: 7 of 11 recognitions are successful. The most informative part of the paper is a summary of the fold-recognition technique used by Sippl's group. The sequence-fold alignment employs dynamic programming to align the target sequence with a fold using a 'frozen approximation', that is, the energy field generated by the original sequence of this fold. The energy functions are derived from protein statistics. A special problem is the optimization of the gap penalties (or, in general, the correct calculation of the 'energetic cost' of the sequence fragment excluded from the sequence-fold alignment). The following remedy is suggested: take a set of preliminary gap penalty energies g′, g″, ...; obtain the corresponding optimal alignments s′:f,s″:f, ..., of investigated sequence, s, with target fold, f (each alignment normally includes
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s′ is the energy dispersion for subsequence s′ computed by a no-gap threading of s′ onto a control set of protein folds: the higher the z-score, the more probable is the alignment, and the more probable is that the native fold of the investigated sequence is similar to the given target fold.
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50
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0023479421
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Why do globular proteins fit the limited set of folding patterns?
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Finkelstein AV, Ptitsyn OB. Why do globular proteins fit the limited set of folding patterns? Progr Biophys Mol Biol. 50:1987;171-190.
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(1987)
Progr Biophys Mol Biol
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Finkelstein, A.V.1
Ptitsyn, O.B.2
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51
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0024279564
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General architecture of α-helical globules
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Murzin AG, Finkelstein AV. General architecture of α-helical globules. J Mol Biol. 204:1988;749-770.
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J Mol Biol
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Murzin, A.G.1
Finkelstein, A.V.2
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52
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0028961335
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SCOP: A structural classification of protein database for the investigation of sequences and structures
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of special interest. The paper presents a description of the database containing a comprehensive classification of protein folds, superfamilies, families, etc.
-
Murzin AG, Brenner SE, Hubbard TJP, Chothia C. SCOP: a structural classification of protein database for the investigation of sequences and structures. of special interest J Mol Biol. 247:1995;534-540 The paper presents a description of the database containing a comprehensive classification of protein folds, superfamilies, families, etc.
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(1995)
J Mol Biol
, vol.247
, pp. 534-540
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Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.J.P.3
Chothia, C.4
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53
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0028838717
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Threading a database of protein cores
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of outstanding interest. A critical analysis of the authors' blind protein-fold recognitions is presented which stresses that a successful fold recognition depends on the accurate definition of those parts of the fold that are, or are not, likely to be conserved in protein evolution.
-
Madej T, Gibart JF, Bryant SH. Threading a database of protein cores. of outstanding interest Proteins. 23:1995;356-369 A critical analysis of the authors' blind protein-fold recognitions is presented which stresses that a successful fold recognition depends on the accurate definition of those parts of the fold that are, or are not, likely to be conserved in protein evolution.
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(1995)
Proteins
, vol.23
, pp. 356-369
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Madej, T.1
Gibart, J.F.2
Bryant, S.H.3
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54
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0029996682
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Search for the most stable folds of protein chains. I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction
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of special interest. The paper presents a general approach to the prediction of 3D folds of protein chains from their amino-acid sequences. It is based on the use of the SCMF theory for long-range interactions, on the use of 1D statistical mechanics for short-range interactions, and on the fact that there are only a relatively small set of 'potentially stable' folding patterns. This makes it possible to examine the whole variety of potentially stable folds and to find the thermodynamically stable structure. The paper contains a detailed presentation of a SCMF theory as applied to protein chains and (as an Appendix) the computer algorithms of 1D statistical mechanics.
-
Finkelstein AV, Reva BA. Search for the most stable folds of protein chains. I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction. of special interest Protein Eng. 9:1996;387-397 The paper presents a general approach to the prediction of 3D folds of protein chains from their amino-acid sequences. It is based on the use of the SCMF theory for long-range interactions, on the use of 1D statistical mechanics for short-range interactions, and on the fact that there are only a relatively small set of 'potentially stable' folding patterns. This makes it possible to examine the whole variety of potentially stable folds and to find the thermodynamically stable structure. The paper contains a detailed presentation of a SCMF theory as applied to protein chains and (as an Appendix) the computer algorithms of 1D statistical mechanics.
-
(1996)
Protein Eng
, vol.9
, pp. 387-397
-
-
Finkelstein, A.V.1
Reva, B.A.2
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55
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0030006836
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Search for the most stable folds of protein chains. II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory
-
of special interest. In this paper, a general SCMF approach is applied to single out the most stable fold for the chains of different β-sandwich proteins. The choice is made from the library of 96 different idealized β-sandwich-folding patterns. The native pattern is found out of 1-3, or sometimes out of 6, patterns having the lowest free energy for this chain (however, the results are much worse for the chains that have very long loops in their native folds). Computing a detailed chain fold within its native folding pattern, one obtains a rather close (although not perfect) similarity of calculated and observed structures.
-
Reva BA, Finkelstein AV. Search for the most stable folds of protein chains. II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory. of special interest Protein Eng. 9:1996;397-411 In this paper, a general SCMF approach is applied to single out the most stable fold for the chains of different β-sandwich proteins. The choice is made from the library of 96 different idealized β-sandwich-folding patterns. The native pattern is found out of 1-3, or sometimes out of 6, patterns having the lowest free energy for this chain (however, the results are much worse for the chains that have very long loops in their native folds). Computing a detailed chain fold within its native folding pattern, one obtains a rather close (although not perfect) similarity of calculated and observed structures.
-
(1996)
Protein Eng
, vol.9
, pp. 397-411
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-
Reva, B.A.1
Finkelstein, A.V.2
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56
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0028803613
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Outline structures for the extracellular domains of the fibroblast growth factor receptors
-
of special interest. The work presented is based on the 'key residues' that are identified in the known 3D structure as those primarily responsible for the structure of the central core of the protein through their packing, hydrogen-bonding or unusual conformations.
-
Bateman A, Chothia C. Outline structures for the extracellular domains of the fibroblast growth factor receptors. of special interest Nat Struct Biol. 2:1995;1068-1074 The work presented is based on the 'key residues' that are identified in the known 3D structure as those primarily responsible for the structure of the central core of the protein through their packing, hydrogen-bonding or unusual conformations.
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(1995)
Nat Struct Biol
, vol.2
, pp. 1068-1074
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Bateman, A.1
Chothia, C.2
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58
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0030067191
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Assigning amino acid sequences to 3-dimensional protein folds
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of outstanding interest. This is a review of the different approaches to fold recognition. The main steps are singled out: creation of a library of 'target' folds; representation of folds; alignment of the probe sequence to the target fold using the sequence-to-fold compatibility function; assessment of significance of compatibility. Various techniques used at each step are compared and the main technical problems to be solved are outlined.
-
Fisher D, Rice D, Bowie JU, Eisenberg D. Assigning amino acid sequences to 3-dimensional protein folds. of outstanding interest FASEB J. 10:1996;126-136 This is a review of the different approaches to fold recognition. The main steps are singled out: creation of a library of 'target' folds; representation of folds; alignment of the probe sequence to the target fold using the sequence-to-fold compatibility function; assessment of significance of compatibility. Various techniques used at each step are compared and the main technical problems to be solved are outlined.
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(1996)
FASEB J
, vol.10
, pp. 126-136
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Fisher, D.1
Rice, D.2
Bowie, J.U.3
Eisenberg, D.4
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59
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0029964055
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Potential energy functions for threading
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of special interest. of outstanding interest. A very clearly written review of the different potential functions used for recognition of tertiary folds. The review concerns both the most simplified residue-energy functions and the sophisticated full-atom ones. The authors stress that although the pairwise interaction potentials mostly encode the residue-solvation preferences, the threading methods based on pairwise interactions work better than the profile-based (i.e. solvation) methods because accessibility is not well conserved in similar folds. Together with [87], the review underlines a parallel between experimental protein folding to a molten-globule state and fold prediction using simplified energy functions. The review ends with the phrase "In experimental folding, attaining correct sidechain packing appears to be rate-limiting step. Let's hope this is not the case for prediction". I am afraid that I believe this hope is weak.
-
of special interest Jones DT, Thornton J. Potential energy functions for threading. of outstanding interest Curr Opin Struct Biol. 6:1996;210-216 A very clearly written review of the different potential functions used for recognition of tertiary folds. The review concerns both the most simplified residue-energy functions and the sophisticated full-atom ones. The authors stress that although the pairwise interaction potentials mostly encode the residue-solvation preferences, the threading methods based on pairwise interactions work better than the profile-based (i.e. solvation) methods because accessibility is not well conserved in similar folds. Together with [87], the review underlines a parallel between experimental protein folding to a molten-globule state and fold prediction using simplified energy functions. The review ends with the phrase "In experimental folding, attaining correct sidechain packing appears to be rate-limiting step. Let's hope this is not the case for prediction". I am afraid that I believe this hope is weak.
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(1996)
Curr Opin Struct Biol
, vol.6
, pp. 210-216
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Jones, D.T.1
Thornton, J.2
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60
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0027305858
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Alignment and search for the common protein folds using a data bank of structural templates
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Johnson MS, Overington J, Blundell TL. Alignment and search for the common protein folds using a data bank of structural templates. J Mol Biol. 231:1993;735-752.
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(1993)
J Mol Biol
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Johnson, M.S.1
Overington, J.2
Blundell, T.L.3
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61
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0027302043
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Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures.
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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.
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(1993)
J Mol Biol
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Ouzounis, C.1
Sander, C.2
Scharf, M.3
Schneider, R.4
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62
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0028318094
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Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
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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.
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(1994)
J Mol Biol
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Kocher, J.P.A.1
Rooman, M.J.2
Wodak, S.J.3
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63
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0029083544
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Detection of protein 3D - 1D compatibility characterised by the evaluation of side-chain packing and electrostatic interactions
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of special interest. The central point of this interesting but rather complicated paper is an attempt to take into account the sidechain packing in protein-fold recognition, that is, to take into account not only the interresidue distance but also the orientation of sidechains.
-
Matsuo Y, Nakamura H, Nishikava K. Detection of protein 3D - 1D compatibility characterised by the evaluation of side-chain packing and electrostatic interactions. of special interest J Biochem (Tokyo). 118:1995;137-148 The central point of this interesting but rather complicated paper is an attempt to take into account the sidechain packing in protein-fold recognition, that is, to take into account not only the interresidue distance but also the orientation of sidechains.
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(1995)
J Biochem (Tokyo)
, vol.118
, pp. 137-148
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Matsuo, Y.1
Nakamura, H.2
Nishikava, K.3
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64
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0028874809
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Assessment of protein fold recognition method that takes into account four physicochemical properties: Side-chain packing, solvation, hydrogen-bonding and local conformations
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of special interest. See annotation [65].
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Matsuo Y, Nishikava K. Assessment of protein fold recognition method that takes into account four physicochemical properties: side-chain packing, solvation, hydrogen-bonding and local conformations. of special interest Proteins. 23:1995;370-375 See annotation [65].
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(1995)
Proteins
, vol.23
, pp. 370-375
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Matsuo, Y.1
Nishikava, K.2
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65
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0028865588
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Successful protein fold recognition by optimal sequence threading validated by rigorous blind test
-
of special interest. This paper, together with [64], analyzes the results of the authors' blind protein-structure recognitions.
-
Jones DT, Miller L, Thornton JM. Successful protein fold recognition by optimal sequence threading validated by rigorous blind test. of special interest Proteins. 23:1995;387-397 This paper, together with [64], analyzes the results of the authors' blind protein-structure recognitions.
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(1995)
Proteins
, vol.23
, pp. 387-397
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-
Jones, D.T.1
Miller, L.2
Thornton, J.M.3
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66
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0028886967
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Inverse protein folding by the residue pair preference method: Estimating the correctness of alignments of structurally compatible sequences
-
of special interest. The method described in this paper combines environmental profiles with the pair-preference based profile; the latter is adjusted in the course of iterative computations. Testing shows that this method gives a 50% (on average) correct alignment when the rmsd between the native folds of target and probe chains is less than 2.
-
Wilmanns M, Eisenberg D. Inverse protein folding by the residue pair preference method: estimating the correctness of alignments of structurally compatible sequences. of special interest Protein Eng. 8:1995;627-639 The method described in this paper combines environmental profiles with the pair-preference based profile; the latter is adjusted in the course of iterative computations. Testing shows that this method gives a 50% (on average) correct alignment when the rmsd between the native folds of target and probe chains is less than 2.
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(1995)
Protein Eng
, vol.8
, pp. 627-639
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Wilmanns, M.1
Eisenberg, D.2
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67
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85030285864
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Evaluation of threading alignments
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of special interest This paper describes a modification of the original 'fingerprint' approach to modelling [47]. The amino-acid environment of each point of the target fold is updated in the course of threading. The authors stress that the choice of gap insertion/deletion penalties is crucial for the quality of threading, and that this problem is yet unsolved. It is shown that sequence alignments are less accurate than threading alignments for distantly related proteins that have a sequence identity of 30% or less
-
Jaroszewski L, Godzik A. Evaluation of threading alignments. of special interest Protein Eng. 1997; This paper describes a modification of the original 'fingerprint' approach to modelling [47]. The amino-acid environment of each point of the target fold is updated in the course of threading. The authors stress that the choice of gap insertion/deletion penalties is crucial for the quality of threading, and that this problem is yet unsolved. It is shown that sequence alignments are less accurate than threading alignments for distantly related proteins that have a sequence identity of 30% or less.
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(1997)
Protein Eng
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Jaroszewski, L.1
Godzik, A.2
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68
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0015244817
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Empirical protein energy maps
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Pohl FM. Empirical protein energy maps. Nature. 234:1971;277-279.
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Nature
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Pohl, F.M.1
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69
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0028801308
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Why do protein architectures have a Boltzmann-like statistics?
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of special interest. A theoretical investigation of the typical statistics of the stable folds of random heteropolymers is performed to explain the basis of a Boltzmann-like form of the statistics of globular proteins. It is shown that the statistics resemble more the correlation functions observed in liquids or solids, in other words, they reflect the energy of interactions within a given element (which dominates when the internal interactions are strong), plus the interaction of this element with the environment. The 'temperature' in these statistics is the freezing temperature of the heteropolymers. The origin of these statistics is simply that the more stable is the element, the more sequences can provide stability to the folds with the element, and, as a result, the more often this element is observed in a random or quasirandom soup of sequences.
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Finkelstein AV, Badretdinov AY, Gutin AM. Why do protein architectures have a Boltzmann-like statistics? of special interest Proteins. 23:1995;142-150 A theoretical investigation of the typical statistics of the stable folds of random heteropolymers is performed to explain the basis of a Boltzmann-like form of the statistics of globular proteins. It is shown that the statistics resemble more the correlation functions observed in liquids or solids, in other words, they reflect the energy of interactions within a given element (which dominates when the internal interactions are strong), plus the interaction of this element with the environment. The 'temperature' in these statistics is the freezing temperature of the heteropolymers. The origin of these statistics is simply that the more stable is the element, the more sequences can provide stability to the folds with the element, and, as a result, the more often this element is observed in a random or quasirandom soup of sequences.
-
(1995)
Proteins
, vol.23
, pp. 142-150
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Finkelstein, A.V.1
Badretdinov, A.Y.2
Gutin, A.M.3
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70
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0029976427
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Statistical potentials extracted from protein structures: How accurate they are?
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of special interest. The results of this paper suggest that current statistical potentials may have a limited value: an exact lattice-model test has shown that these potentials often rank in order the true relative strengths of interresidue interactions correctly, but (at least for the investigated chains composed of two sorts of residues: in such chains the many-body effects are most visible [69,110]) they do not correctly reflect the true underlying energies.
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Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate they are? of special interest J Mol Biol. 257:1995;457-469 The results of this paper suggest that current statistical potentials may have a limited value: an exact lattice-model test has shown that these potentials often rank in order the true relative strengths of interresidue interactions correctly, but (at least for the investigated chains composed of two sorts of residues: in such chains the many-body effects are most visible [69,110]) they do not correctly reflect the true underlying energies.
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(1995)
J Mol Biol
, vol.257
, pp. 457-469
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Thomas, P.D.1
Dill, K.A.2
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71
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0029563695
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Are database-derived potentials valid for the scoring both forward and inverted protein folding?
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of special interest. The paper shows a way to correct the database-derived potentials for the many-body effects and stresses the necessity of this correction.
-
Rooman M, Wodak S. Are database-derived potentials valid for the scoring both forward and inverted protein folding? of special interest Protein Eng. 8:1995;849-858 The paper shows a way to correct the database-derived potentials for the many-body effects and stresses the necessity of this correction.
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(1995)
Protein Eng
, vol.8
, pp. 849-858
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Rooman, M.1
Wodak, S.2
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72
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0028892389
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Are proteins ideal mixtures of amino acids? Analysis of energy parameter set
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of outstanding interest. This paper presents a very useful comparative analysis of various popular sets of mean-force two-body potentials that are based on protein structures. The authors show that the difference between these sets can be traced to the difference in a reference state used to define the zero energy. After a correction for this difference, various sets of potentials correlate at the level of 50-80%, although before the correction the correlation was much worse. In addition, the authors point to a good correlation of potentials derived from big and small proteins, and to an unexplained bad correlation between the potentials derived from crystallographic protein structures and those derived from NMR structure.
-
Godzik A, Kolinski A, Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter set. of outstanding interest Protein Sci. 4:1995;2107-2117 This paper presents a very useful comparative analysis of various popular sets of mean-force two-body potentials that are based on protein structures. The authors show that the difference between these sets can be traced to the difference in a reference state used to define the zero energy. After a correction for this difference, various sets of potentials correlate at the level of 50-80%, although before the correction the correlation was much worse. In addition, the authors point to a good correlation of potentials derived from big and small proteins, and to an unexplained bad correlation between the potentials derived from crystallographic protein structures and those derived from NMR structure.
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(1995)
Protein Sci
, vol.4
, pp. 2107-2117
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Godzik, A.1
Kolinski, A.2
Skolnick, J.3
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73
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0029942661
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Structure-derived potentials and protein simulations
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of special interest. A critical review of knowledge-based mean-force potentials. The review stresses that a correct determination of a 'reference state' (e.g. 'residues dissolved in water' or 'residues dissolved in a random mixture of amino acids') is critically important for successful application of the potential functions.
-
Jernigan R, Bahar I. Structure-derived potentials and protein simulations. of special interest Curr Opin Struct Biol. 6:1996;195-209 A critical review of knowledge-based mean-force potentials. The review stresses that a correct determination of a 'reference state' (e.g. 'residues dissolved in water' or 'residues dissolved in a random mixture of amino acids') is critically important for successful application of the potential functions.
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(1996)
Curr Opin Struct Biol
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Jernigan, R.1
Bahar, I.2
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74
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Maiorov VN, Crippen GM. Contact potential that recognises the correct folding of globular proteins. J Mol Biol. 227:1992;876-888.
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Maiorov, V.N.1
Crippen, G.M.2
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75
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0029895539
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Self-consistently optimised statistical mechanical energy functions for sequence structure alignment
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of outstanding interest. This paper describes an optimization of energy functions and their application to the discrimination of correctly folded protein chains from the misfolded ones. The main idea of the optimization [22] is that the optimal energy functions can be obtained by maximising the ratio of the stability gap, between the average energy of the correct fold and the mean energy of the full ensemble of misfolded structures, to the standard deviation of energies of the misfolded structures.
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Koretke KK, Luthey-Schulten ZA, Wolynes PG. Self-consistently optimised statistical mechanical energy functions for sequence structure alignment. of outstanding interest Protein Sci. 5:1996;1043-1059 This paper describes an optimization of energy functions and their application to the discrimination of correctly folded protein chains from the misfolded ones. The main idea of the optimization [22] is that the optimal energy functions can be obtained by maximising the ratio of the stability gap, between the average energy of the correct fold and the mean energy of the full ensemble of misfolded structures, to the standard deviation of energies of the misfolded structures.
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(1996)
Protein Sci
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Koretke, K.K.1
Luthey-Schulten, Z.A.2
Wolynes, P.G.3
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76
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Recognition of distantly related proteins through energy calculations
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Abagyan R, Frishman D, Argos P. Recognition of distantly related proteins through energy calculations. Proteins. 19:1994;132-140.
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(1994)
Proteins
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Abagyan, R.1
Frishman, D.2
Argos, P.3
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Minor DL Jr, Kim PS. Context is a major determinant of β-sheet propensity. Nature. 371:1994;264-267.
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Nature
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Minor D.L., Jr.1
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Galzitskaya OV, Finkelstein AV. Folding of chains with random and edited sequences: similarities and differences. Protein Eng. 8:1995;883-892.
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Galzitskaya, O.V.1
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of special interest. Chapman & Hall, London, An excellent, but not an easy, mathematical book for biologists that contains not only theorems but also numerous algorithms. For a reader of this review, the most relevant chapters are 9-12, which deals with dynamic-programming algorithms, pattern probabilities and statistics
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Waterman MS. . of special interest Introduction to Computational Biology. Maps, Sequences and Genomes. 1995;Chapman & Hall, London, An excellent, but not an easy, mathematical book for biologists that contains not only theorems but also numerous algorithms. For a reader of this review, the most relevant chapters are 9-12, which deals with dynamic-programming algorithms, pattern probabilities and statistics.
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Introduction to Computational Biology. Maps, Sequences and Genomes
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of outstanding interest. This paper describes a new approach which simultaneously calculates loop conformation and sidechain positioning in homology modelling. It uses a database of possible loop conformations, a rotamer sidechain library, and an iterative refinement based on the SCMF theory.
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Koehl P, Delarue M. A self-consistent mean-field approach to simultaneous gap closure and side-chain positioning in homology modelling. of outstanding interest Nat Struct Biol. 2:1995;163-170 This paper describes a new approach which simultaneously calculates loop conformation and sidechain positioning in homology modelling. It uses a database of possible loop conformations, a rotamer sidechain library, and an iterative refinement based on the SCMF theory.
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Koehl, P.1
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91
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of special interest. This review gives a simple description of SCMF theory and describes a number of applications of this theory to problems of protein-structure prediction, especially the prediction of the sidechain conformations within a given protein fold.
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Koehl P, Delarue M. Mean-field minimisation methods for biological macromolecules. of special interest Curr Opin Struct Biol. 6:1996;222-226 This review gives a simple description of SCMF theory and describes a number of applications of this theory to problems of protein-structure prediction, especially the prediction of the sidechain conformations within a given protein fold.
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Laurents DV, Subbiah S, Levitt M. Different protein sequences can give rise to highly similar folds through different stabilising interactions. Protein Sci. 3:1994;1938-1944.
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93
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Evaluation of threading specificity and accuracy
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of special interest. A threading experiment using globins shows that a sequence can recognize, as a cognate, the fold of its remote homologue only when the native fold of this sequence and the fold of the homologue have at least 60% of super-imposible analogous residue sites. Not all the pairs of globins satisfy this condition. Threading alignment is even more sensitive to structure similarity (the alignment places the majority of residues correctly only when a deviation of superimposed-residue sites is less than 2 Å).
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Bryant SH. Evaluation of threading specificity and accuracy. of special interest Proteins. 26:1996;172-185 A threading experiment using globins shows that a sequence can recognize, as a cognate, the fold of its remote homologue only when the native fold of this sequence and the fold of the homologue have at least 60% of super-imposible analogous residue sites. Not all the pairs of globins satisfy this condition. Threading alignment is even more sensitive to structure similarity (the alignment places the majority of residues correctly only when a deviation of superimposed-residue sites is less than 2 Å).
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Proteins
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Chothia C. One thousand protein families for the molecular biologist. Nature. 357:1992;543-544.
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TOPITS: Threading one-dimensional predictions into three-dimensional structure
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of special interest. AAA Press, Menlo Park, The paper describes a simplified threading approach based the on alignments of predicted (using PHD [31]) secondary structures and predicted residue accessibilities with those observed in proteins of known 3D structure
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Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structure. of special interest ISMB-95: Proceedings of the 3rd Internatal Conference on Intelligent Systems for Molecular Biology. 1995;314-320 AAA Press, Menlo Park, The paper describes a simplified threading approach based the on alignments of predicted (using PHD [31]) secondary structures and predicted residue accessibilities with those observed in proteins of known 3D structure.
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Hubbard JT, Park J. Fold recognition and ab initio structure prediction using hidden Markov models and -strand pair profiles. Proteins. 23:1995;398-402.
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of special interest. A review of kinetic and thermodynamic folding intermediates, which gives special attention to the native like highly-ordered molten globules, to the looser premolten globules, and to the barrier between them.
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Ptitsyn OB. Structures of folding intermediates. of special interest Curr Opin Struct Biol. 5:1995;74-78 A review of kinetic and thermodynamic folding intermediates, which gives special attention to the native like highly-ordered molten globules, to the looser premolten globules, and to the barrier between them.
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of outstanding interest. A comprehensive review describing the present state of studies of the molten globule state and its role in protein folding and in physiological processes.
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Ptitsyn OB. Molten globule and protein folding. of outstanding interest Adv Prot Chem. 47:1995;83-229 A comprehensive review describing the present state of studies of the molten globule state and its role in protein folding and in physiological processes.
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of special interest. The described method uses very few energy parameters: one for hydrophobic interactions of nonpolar atoms; another for interaction of the hydrogen-bond donors and acceptors; and the hard-sphere van der Waals radii parameters. Amino acids are represented as 'united atoms', except for polar hydrogens, which are explicit. Each amino acid has between 3 (for proline) to 6 (for glycine) possible mainchain conformations. A new very fast 'constraint-based exhaustive' searching method is used to look through all the possible compact conformations. For the four small proteins examined, this method finds a relatively small number of low-energy conformations, among which are native-like folds. The rmsd of these native-like folds from the native ones is 4-5.
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Yue K, Dill KA. Folding proteins with simple energy function and extensive conformational searching. of special interest Protein Sci. 5:1996;254-261 The described method uses very few energy parameters: one for hydrophobic interactions of nonpolar atoms; another for interaction of the hydrogen-bond donors and acceptors; and the hard-sphere van der Waals radii parameters. Amino acids are represented as 'united atoms', except for polar hydrogens, which are explicit. Each amino acid has between 3 (for proline) to 6 (for glycine) possible mainchain conformations. A new very fast 'constraint-based exhaustive' searching method is used to look through all the possible compact conformations. For the four small proteins examined, this method finds a relatively small number of low-energy conformations, among which are native-like folds. The rmsd of these native-like folds from the native ones is 4-5.
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Protein Sci
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of special interest. This paper shows that a successful folding requires a sufficiently large energy gap between the lowest energy fold and the other ones. The decrease of probability of a successful folding with a growth of inaccuracy of potentials results from the average decrease of this gap.
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De Araujo AFP, Pochepski TC. Monte Carlo simulations of protein folding using unexact potentials; how accurate must parameters be in order to preserve the essential features of energy landscape? of special interest Fold Des. 1:1996;299-314 This paper shows that a successful folding requires a sufficiently large energy gap between the lowest energy fold and the other ones.
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