-
1
-
-
36749030503
-
High accuracy template based modeling by global optimization
-
Joo K, Lee J, Lee S, Seo JH, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins 2007;69:83–89.
-
(2007)
Proteins
, vol.69
, pp. 83-89
-
-
Joo, K.1
Lee, J.2
Lee, S.3
Seo, J.H.4
Lee, S.J.5
Lee, J.6
-
2
-
-
74249090260
-
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
-
Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins 2009;77:114–122.
-
(2009)
Proteins
, vol.77
, pp. 114-122
-
-
Krieger, E.1
Joo, K.2
Lee, J.3
Lee, J.4
Raman, S.5
Thompson, J.6
Tyka, M.7
Baker, D.8
Karplus, K.9
-
3
-
-
84893009061
-
Protein structure modeling for CASP10 by multiple layers of global optimization
-
Joo K, Lee J, Sim S, Lee SY, Lee K, Heo S, Lee IH, Lee SJ, Lee J. Protein structure modeling for CASP10 by multiple layers of global optimization. Proteins 2014;82:188–195.
-
(2014)
Proteins
, vol.82
, pp. 188-195
-
-
Joo, K.1
Lee, J.2
Sim, S.3
Lee, S.Y.4
Lee, K.5
Heo, S.6
Lee, I.H.7
Lee, S.J.8
Lee, J.9
-
4
-
-
0001176785
-
New optimization method for conformational energy calculations on polypeptides: conformational space annealing
-
Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J Comput Chem 1997;18:1222–1232.
-
(1997)
J Comput Chem
, vol.18
, pp. 1222-1232
-
-
Lee, J.1
Scheraga, H.A.2
Rackovsky, S.3
-
5
-
-
0032146482
-
Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
-
Lee J, Scheraga HA, Rackovsky S. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 1998;46:103–116.
-
(1998)
Biopolymers
, vol.46
, pp. 103-116
-
-
Lee, J.1
Scheraga, H.A.2
Rackovsky, S.3
-
6
-
-
0032605909
-
Calculation of protein conformation by global optimization of a potential energy function
-
Lee J, Liwo A, Ripoll DR, Pillardy J, Scheraga HA. Calculation of protein conformation by global optimization of a potential energy function. Proteins 1999; (Suppl 3):204–208.
-
(1999)
Proteins
, pp. 204-208
-
-
Lee, J.1
Liwo, A.2
Ripoll, D.R.3
Pillardy, J.4
Scheraga, H.A.5
-
7
-
-
0002001599
-
Hierarchical energy-based approach to protein-structure prediction: blind-test evaluation with casp3 targets
-
Lee J, Liwo A, Ripoll DR, Pillardy J, Gibson KD, Saunders JA, Scheraga HA. Hierarchical energy-based approach to protein-structure prediction: blind-test evaluation with casp3 targets. J Comput Chem 2000;77:90–117.
-
(2000)
J Comput Chem
, vol.77
, pp. 90-117
-
-
Lee, J.1
Liwo, A.2
Ripoll, D.R.3
Pillardy, J.4
Gibson, K.D.5
Saunders, J.A.6
Scheraga, H.A.7
-
8
-
-
0000542451
-
Conformational space annealing by parallel computations: extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin
-
Lee J, Scheraga HA. Conformational space annealing by parallel computations: extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin. Int J Quantum Chem 1999;75:255–265.
-
(1999)
Int J Quantum Chem
, vol.75
, pp. 255-265
-
-
Lee, J.1
Scheraga, H.A.2
-
9
-
-
0141904480
-
Unbiased global optimization of Lennard-Jones clusters for n ≤ 201 using the conformational space annealing method
-
Lee J, Lee IH, Lee J. Unbiased global optimization of Lennard-Jones clusters for n ≤ 201 using the conformational space annealing method. Phys Rev Lett 2003;91:080201.
-
(2003)
Phys Rev Lett
, vol.91
, pp. 080201.
-
-
Lee, J.1
Lee, I.H.2
Lee, J.3
-
10
-
-
58149279530
-
Multiple sequence alignment by conformational space annealing
-
Joo K, Lee J, Kim I, Lee SJ, Lee J. Multiple sequence alignment by conformational space annealing. Biophys J 2008;95:4813–4819.
-
(2008)
Biophys J
, vol.95
, pp. 4813-4819
-
-
Joo, K.1
Lee, J.2
Kim, I.3
Lee, S.J.4
Lee, J.5
-
11
-
-
69849109596
-
All-atom chain-building by optimizing MODELLER energy function using conformational space annealing
-
Joo K, Lee J, Seo JH, Lee K, Kim BG, Lee J. All-atom chain-building by optimizing MODELLER energy function using conformational space annealing. Proteins 2009;75:1010–1023.
-
(2009)
Proteins
, vol.75
, pp. 1010-1023
-
-
Joo, K.1
Lee, J.2
Seo, J.H.3
Lee, K.4
Kim, B.G.5
Lee, J.6
-
12
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005;21:951–960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
13
-
-
0142192295
-
-
Conditional random fields Probabilistic models for segmenting and labeling sequence data. In Proceeding of the 18th International Conference on Machine Learning. San Francisco, CA, USA Morgan Kaufmann Publishers Inc., pp
-
Lafferty J, McCallum A, Pereira F. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. In: Proceeding of the 18th International Conference on Machine Learning. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc. 2001. pp 282–289.
-
(2001)
, pp. 282-289
-
-
Lafferty, J.1
McCallum, A.2
Pereira, F.3
-
14
-
-
0035470889
-
Greedy function approximation: a gradient boosting machine
-
Friedman JH. Greedy function approximation: a gradient boosting machine. Ann Stat 2001;29:1189–1232.
-
(2001)
Ann Stat
, vol.29
, pp. 1189-1232
-
-
Friedman, J.H.1
-
15
-
-
67650439454
-
Boosting protein threading accuracy. Research in computational molecular biology:… Annual International Conference, RECOMB…: proceedings
-
Peng J, Xu J. Boosting protein threading accuracy. Research in computational molecular biology:… Annual International Conference, RECOMB…: proceedings. Int Conf Res Comput Mol Biol 2009;5541:31–45.
-
(2009)
Int Conf Res Comput Mol Biol
, vol.5541
, pp. 31-45
-
-
Peng, J.1
Xu, J.2
-
16
-
-
16344394781
-
SABmarka benchmark for sequence alignment that covers the entire known fold space
-
Walle IV, Lasters I, Wyns L. SABmarka benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005;21:1267–1268.
-
(2005)
Bioinformatics
, vol.21
, pp. 1267-1268
-
-
Walle, I.V.1
Lasters, I.2
Wyns, L.3
-
17
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov GG, Shapovalov MV, Dunbrack RL. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009;77:778–795.
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack, R.L.3
-
18
-
-
84892959896
-
Assessment of template-based protein structure predictions in CASP10
-
Huang YJ, Mao B, Aramini JM, Montelione GT. Assessment of template-based protein structure predictions in CASP10. Proteins 2014;82:43–56.
-
(2014)
Proteins
, vol.82
, pp. 43-56
-
-
Huang, Y.J.1
Mao, B.2
Aramini, J.M.3
Montelione, G.T.4
-
19
-
-
85086677973
-
-
Sequence-structure alignment of proteins based on conditional random fields with structural scores
-
Lee SJ, Joo K, Sim S, Lee J, Lee I-H, Lee J. Sequence-structure alignment of proteins based on conditional random fields with structural scores.
-
-
-
Lee, S.J.1
Joo, K.2
Sim, S.3
Lee, J.4
Lee, I.-H.5
Lee, J.6
-
20
-
-
67650439454
-
Boosting protein threading accuracy
-
Peng J, Xu J. Boosting protein threading accuracy. Res Comput Mol Biol 2009;5541:31–45.
-
(2009)
Res Comput Mol Biol
, vol.5541
, pp. 31-45
-
-
Peng, J.1
Xu, J.2
-
21
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702–710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
22
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195–202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
23
-
-
84862184719
-
Sann: solvent accessibility prediction of proteins by nearest neighbor method
-
Joo K, Lee SJ, Lee J. Sann: solvent accessibility prediction of proteins by nearest neighbor method. Proteins 2012;80:1791–1797.
-
(2012)
Proteins
, vol.80
, pp. 1791-1797
-
-
Joo, K.1
Lee, S.J.2
Lee, J.3
-
24
-
-
22944458570
-
Fold recognition by predicted alignment accuracy
-
Xu J. Fold recognition by predicted alignment accuracy. IEEE/ACM Trans Comput Biol Bioinformatics 2005;2:157–165.
-
(2005)
IEEE/ACM Trans Comput Biol Bioinformatics
, vol.2
, pp. 157-165
-
-
Xu, J.1
-
25
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992;256:1443–1445.
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
26
-
-
33746239564
-
Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences
-
Tan YH, Huang H, Kihara D. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins 2006;64:587–600.
-
(2006)
Proteins
, vol.64
, pp. 587-600
-
-
Tan, Y.H.1
Huang, H.2
Kihara, D.3
-
27
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915–10919.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
28
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22:1658–1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
29
-
-
84861945707
-
Modularity optimization by conformational space annealing
-
Lee J, Gross SP, Lee J. Modularity optimization by conformational space annealing. Phys Rev E 2012;85:056702.
-
(2012)
Phys Rev E
, vol.85
, pp. 056702.
-
-
Lee, J.1
Gross, S.P.2
Lee, J.3
-
30
-
-
84880388848
-
Improved network community structure improves function prediction
-
Lee J, Gross SP, Lee J. Improved network community structure improves function prediction. Scientific Rep 2013;3.
-
(2013)
Scientific Rep
, vol.3
-
-
Lee, J.1
Gross, S.P.2
Lee, J.3
-
31
-
-
84875959983
-
Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction
-
Lee J, Lee J. Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction. PLoS One 2013;8:e60372.
-
(2013)
PLoS One
, vol.8
-
-
Lee, J.1
Lee, J.2
-
32
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779–815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
33
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, AD, Bashford D, Bellott M, Dunbrack, RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586–3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
34
-
-
79960101915
-
De novo protein structure prediction by dynamic fragment assembly and conformational space annealing
-
Lee J, Lee J, Sasaki TN, Sasai M, Seok C, Lee J. De novo protein structure prediction by dynamic fragment assembly and conformational space annealing. Proteins 2011;79:2403–2417.
-
(2011)
Proteins
, vol.79
, pp. 2403-2417
-
-
Lee, J.1
Lee, J.2
Sasaki, T.N.3
Sasai, M.4
Seok, C.5
Lee, J.6
-
35
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714–2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
36
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239–1259.
-
(2003)
J Mol Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
37
-
-
80054694711
-
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction
-
Zhou H, Skolnick J. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J 2011;101:2043–2052.
-
(2011)
Biophys J
, vol.101
, pp. 2043-2052
-
-
Zhou, H.1
Skolnick, J.2
-
38
-
-
85057928955
-
Template free modeling by lee and leer in casp11
-
in press
-
Joung, I, Lee, SY, Cheng, Q, Joo, K, Lee, SJ, Lee, J. Template free modeling by lee and leer in casp11. Proteins, in press.
-
Proteins
-
-
Joung, I.1
Lee, S.Y.2
Cheng, Q.3
Joo, K.4
Lee, S.J.5
Lee, J.6
-
39
-
-
85086650484
-
Contact assisted protein structure modeling by global optimization in casp11 experiments
-
in press
-
Joo, K, Joung, I, Cheng, Q, Lee, SJ, Lee, J. Contact assisted protein structure modeling by global optimization in casp11 experiments. Proteins, in press.
-
Proteins
-
-
Joo, K.1
Joung, I.2
Cheng, Q.3
Lee, S.J.4
Lee, J.5
-
40
-
-
84925402614
-
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest
-
Lee J, Lee K, Joung I, Joo K, Brooks BR, Lee J. Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. BMC Bioinformatics 2015;16:94.
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 94.
-
-
Lee, J.1
Lee, K.2
Joung, I.3
Joo, K.4
Brooks, B.R.5
Lee, J.6
-
42
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302–2309.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
43
-
-
84885990516
-
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
-
Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics 2013;29:2722–2728.
-
(2013)
Bioinformatics
, vol.29
, pp. 2722-2728
-
-
Mariani, V.1
Biasini, M.2
Barbato, A.3
Schwede, T.4
-
44
-
-
36749059956
-
Assessment of CASP7 predictions in the high accuracy template-based modeling category
-
Read RJ, Chavali G. Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 2007;69:27–37.
-
(2007)
Proteins
, vol.69
, pp. 27-37
-
-
Read, R.J.1
Chavali, G.2
-
45
-
-
74249092329
-
The other 90% of the protein: assessment beyond the Cs for CASP8 template-based and high-accuracy models
-
Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Cs for CASP8 template-based and high-accuracy models. Proteins 2009;77:29–49.
-
(2009)
Proteins
, vol.77
, pp. 29-49
-
-
Keedy, D.A.1
Williams, C.J.2
Headd, J.J.3
Arendall, W.B.4
Chen, V.B.5
Kapral, G.J.6
Gillespie, R.A.7
Block, J.N.8
Zemla, A.9
Richardson, D.C.10
Richardson, J.S.11
-
46
-
-
84862225232
-
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
-
Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 2012;80:1715–1735.
-
(2012)
Proteins
, vol.80
, pp. 1715-1735
-
-
Xu, D.1
Zhang, Y.2
|