-
3
-
-
0036667733
-
Knowledge-based potential functions in protein design
-
Russ WP, Ranganathan R. Knowledge-based potential functions in protein design. Curr Opin Struct Biol 2002;12:447-452.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 447-452
-
-
Russ, W.P.1
Ranganathan, R.2
-
4
-
-
0035956886
-
Recent improvements in prediction of protein structure by global optimization of a potential energy function
-
Pillardy J, Czaplewski C, Liwo A, Lee J, Ripoll DR, Kamierkiewicz R, Odziej S, Wedemeyer WJ, Gibson KD, Arnautova YA, Saunders J, Ye YJ, Scheraga HA. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci USA 2001;98:2329-2333.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 2329-2333
-
-
Pillardy, J.1
Czaplewski, C.2
Liwo, A.3
Lee, J.4
Ripoll, D.R.5
Kamierkiewicz, R.6
Odziej, S.7
Wedemeyer, W.J.8
Gibson, K.D.9
Arnautova, Y.A.10
Saunders, J.11
Ye, Y.J.12
Scheraga, H.A.13
-
5
-
-
0242299185
-
TOUCHSTONE: A unified approach to protein structure prediction
-
Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki A, Szilagyi A, Kihara D. TOUCHSTONE: a unified approach to protein structure prediction. Proteins 2003;53:469-479.
-
(2003)
Proteins
, vol.53
, pp. 469-479
-
-
Skolnick, J.1
Zhang, Y.2
Arakaki, A.K.3
Kolinski, A.4
Boniecki, A.5
Szilagyi, A.6
Kihara, D.7
-
7
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975;253:694-698.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
8
-
-
0017157584
-
A simplified representation of protein conformation for rapid simulation of protein folding
-
Levitt M. A simplified representation of protein conformation for rapid simulation of protein folding. J Mol Biol 1976;104:59-107.
-
(1976)
J Mol Biol
, vol.104
, pp. 59-107
-
-
Levitt, M.1
-
9
-
-
33646786723
-
Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors
-
Zhang J, Chen R, Liang J. Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins 2006;63:949-960.
-
(2006)
Proteins
, vol.63
, pp. 949-960
-
-
Zhang, J.1
Chen, R.2
Liang, J.3
-
10
-
-
0017021957
-
Medium and long range interaction parameters between amino acids for predicting three dimensional structures of proteins
-
Tanaka S, Scheraga HA. Medium and long range interaction parameters between amino acids for predicting three dimensional structures of proteins. Macromolecules 1976;9:925-950.
-
(1976)
Macromolecules
, vol.9
, pp. 925-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
11
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 1985;18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
12
-
-
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 1996;256:623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
13
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
-
(1997)
J Mol Biol
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
14
-
-
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, Floeckner 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 1990;216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
15
-
-
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 1992;277:676-888.
-
(1992)
J Mol Biol
, vol.277
, pp. 676-888
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
16
-
-
0030983768
-
Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct?
-
Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct? Protein Sci 1997;6:676-688.
-
(1997)
Protein Sci
, vol.6
, pp. 676-688
-
-
Skolnick, J.1
Jaroszewski, L.2
Kolinski, A.3
Godzik, A.4
-
17
-
-
0033970623
-
Derivation of protein-specific pair potentials based on weak sequence fragment similarity
-
Skolnick J, Kolinski A, Ortiz A. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 2000;38:3-16.
-
(2000)
Proteins
, vol.38
, pp. 3-16
-
-
Skolnick, J.1
Kolinski, A.2
Ortiz, A.3
-
18
-
-
0030596063
-
How to derive a protein folding potentials? A new approach to an old problem
-
Mirny LA, Shakhnovich EI. How to derive a protein folding potentials? A new approach to an old problem. J Mol Biol 1996;264:1164-1179.
-
(1996)
J Mol Biol
, vol.264
, pp. 1164-1179
-
-
Mirny, L.A.1
Shakhnovich, E.I.2
-
19
-
-
0029909384
-
An interative method for extracting energy-like quantities from protein structures
-
Thomas PD, Dill KA. An interative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci USA 1996;93:11628-11633.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 11628-11633
-
-
Thomas, P.D.1
Dill, K.A.2
-
20
-
-
0034237798
-
On the design and analysis of protein folding potentials
-
Tobi D, Shafran G, Linial N, Elber R. On the design and analysis of protein folding potentials. Proteins 2000;40:71-85.
-
(2000)
Proteins
, vol.40
, pp. 71-85
-
-
Tobi, D.1
Shafran, G.2
Linial, N.3
Elber, R.4
-
21
-
-
0035865950
-
Learning effective amino acid interactions through iterative stochastic techniques
-
Micheletti C, Seno F, Banavar JR, Maritan A. Learning effective amino acid interactions through iterative stochastic techniques. Proteins 2001;42:422-431.
-
(2001)
Proteins
, vol.42
, pp. 422-431
-
-
Micheletti, C.1
Seno, F.2
Banavar, J.R.3
Maritan, A.4
-
22
-
-
0030968991
-
Empirical potentials and functions for protein folding and binding
-
Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 1997;7:222-228.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 222-228
-
-
Vajda, S.1
Sippl, M.2
Novotny, J.3
-
23
-
-
0030584681
-
Knowledge-based potentials for protein folding: What can we learn from known protein structures?
-
Godzik A. Knowledge-based potentials for protein folding: what can we learn from known protein structures? Structure 1996;4:363-366.
-
(1996)
Structure
, vol.4
, pp. 363-366
-
-
Godzik, A.1
-
24
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996;6:195-209.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
25
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
26
-
-
0033117762
-
Designing potential energy functions for protein folding
-
Hao MH, Scheraga HA, Designing potential energy functions for protein folding. Curr Opin Struct Biol 1999;9:184-188.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 184-188
-
-
Hao, M.H.1
Scheraga, H.A.2
-
27
-
-
0033566967
-
Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition
-
Miyazawa S, Jernigan RL. Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition. Proteins 199936:347-356.
-
(1999)
Proteins
, vol.36
, pp. 347-356
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
28
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 1997;29:292-308.
-
(1997)
Proteins
, vol.29
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
29
-
-
0033867374
-
Identifying sequence-structure pairs undetected by sequence alignments
-
Miyazawa S, Jernigan RL. Identifying sequence-structure pairs undetected by sequence alignments. Protein Eng 2000;13:459-475.
-
(2000)
Protein Eng
, vol.13
, pp. 459-475
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
30
-
-
0037233452
-
Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space
-
Miyazawa S, Jernigan RL. Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space. Proteins 2003;50:35-43.
-
(2003)
Proteins
, vol.50
, pp. 35-43
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
31
-
-
22944468214
-
How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?
-
Miyazawa S, Jernigan RL. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? J Chem Phys 2005;22: 024901.
-
(2005)
J Chem Phys
, vol.22
, pp. 024901
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
32
-
-
14644410346
-
Inferring ideal amino acid interaction forms from statistical protein contact potentials
-
Pokarowski P, Kloczkowski A, Jernigan RL, Kothari NS, Pokarowska M, Kolinski A. Inferring ideal amino acid interaction forms from statistical protein contact potentials. Proteins 2005;59:49-57.
-
(2005)
Proteins
, vol.59
, pp. 49-57
-
-
Pokarowski, P.1
Kloczkowski, A.2
Jernigan, R.L.3
Kothari, N.S.4
Pokarowska, M.5
Kolinski, A.6
-
33
-
-
0034141931
-
Can a pairwise contact potentials stabilize native protein folds against decoys obtained by threading?
-
Vendruscolo M, Najmanovich R Domany E. Can a pairwise contact potentials stabilize native protein folds against decoys obtained by threading? Proteins 2000;38:134-148.
-
(2000)
Proteins
, vol.38
, pp. 134-148
-
-
Vendruscolo, M.1
Najmanovich, R.2
Domany, E.3
-
34
-
-
0035943455
-
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
-
Cater CW, Jr, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 2001;311:625-638.
-
(2001)
J Mol Biol
, vol.311
, pp. 625-638
-
-
Cater Jr, C.W.1
LeFebvre, B.C.2
Cammer, S.A.3
Tropsha, A.4
Edgell, M.H.5
-
35
-
-
0033005899
-
Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
-
Betancourt MR, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999;8:361-369.
-
(1999)
Protein Sci
, vol.8
, pp. 361-369
-
-
Betancourt, M.R.1
Thirumalai, D.2
-
36
-
-
0030806961
-
Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
-
Munson PJ, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 1997;6:1467-1481.
-
(1997)
Protein Sci
, vol.6
, pp. 1467-1481
-
-
Munson, P.J.1
Singh, R.K.2
-
37
-
-
19544391428
-
Geometric cooperativity and anticooperativity of three-body interactions in native proteins
-
Li X, Liang J. Geometric cooperativity and anticooperativity of three-body interactions in native proteins. Proteins 2005;60: 46-65.
-
(2005)
Proteins
, vol.60
, pp. 46-65
-
-
Li, X.1
Liang, J.2
-
38
-
-
0042889108
-
Development of a four-body statistical pseudo-potential to discriminate native from nonnative protein conformations
-
Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from nonnative protein conformations. Bioinformatics 2003;19:1540-1548.
-
(2003)
Bioinformatics
, vol.19
, pp. 1540-1548
-
-
Krishnamoorthy, B.1
Tropsha, A.2
-
39
-
-
33847261239
-
The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions
-
Spassov VZ, Yan L, Flook PK. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions. Protein Sci 2007;16:1-13.
-
(2007)
Protein Sci
, vol.16
, pp. 1-13
-
-
Spassov, V.Z.1
Yan, L.2
Flook, P.K.3
-
40
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr, R.L.2
-
42
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
43
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
-
(1993)
J Appl Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
44
-
-
34249937756
-
-
Hubbard SJ, Thornton JM. NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College London, London; 1993.
-
Hubbard SJ, Thornton JM. NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College London, London; 1993.
-
-
-
-
45
-
-
0033853177
-
Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
-
Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
46
-
-
0032612579
-
-
Simon KT, Bonneau R, Ruczinski I, Baker D. Ab Initio protein structure prediction of CASPIII targets using ROSETTA. Proteins: Struct Funct Genet 1999;3:171-176. Also available at http://depts.washington.edu/bakerpg/decoys/
-
Simon KT, Bonneau R, Ruczinski I, Baker D. Ab Initio protein structure prediction of CASPIII targets using ROSETTA. Proteins: Struct Funct Genet 1999;3:171-176. Also available at http://depts.washington.edu/bakerpg/decoys/
-
-
-
|