-
1
-
-
33846334081
-
Protein structure prediction: The next generation
-
Prentiss MC, Hardin C, Eastwood MP, Zong C, Wolynes PG, Protein structure prediction: The next generation, J Chem Theory Comput 2(3):705-716, 2006.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, Issue.3
, pp. 705-716
-
-
Prentiss, M.C.1
Hardin, C.2
Eastwood, M.P.3
Zong, C.4
Wolynes, P.G.5
-
2
-
-
1842298212
-
From levinthal to pathways to funnels
-
Dill KA, Chan HS, From levinthal to pathways to funnels, Nat Struct Biol 4(1):10-19, 1997.
-
(1997)
Nat. Struct. Biol.
, vol.4
, Issue.1
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
3
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P, Misura KMS, Baker D, Toward high-resolution de novo structure prediction for small proteins, Science 309(5742):1868-1871, 2005.
-
(2005)
Science
, vol.309
, Issue.5742
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
4
-
-
58149277688
-
Guiding conformation space search with an all-Atom energy potential
-
Brunette TJ, Brock O, Guiding conformation space search with an all-Atom energy potential, Proteins: Struct Funct Bioinf 73(4):958-972, 2009.
-
(2009)
Proteins: Struct. Funct. Bioinf.
, vol.73
, Issue.4
, pp. 958-972
-
-
Brunette, T.J.1
Brock, O.2
-
5
-
-
39149100599
-
Coarse-grained models of protein folding: Toy-models or predictive tools
-
Clementi C, Coarse-grained models of protein folding: Toy-models or predictive tools? Curr Opinion Struct Biol 18:10-15, 2008.
-
(2008)
Curr. Opinion. Struct. Biol.
, vol.18
, pp. 10-15
-
-
Clementi, C.1
-
6
-
-
49049098242
-
A stochastic method for the reconstruction of protein structures from one-dimensional structural proles
-
Wol® K, Vendruscolo M, Porto M, A stochastic method for the reconstruction of protein structures from one-dimensional structural proles, Gene 422(1-2):47-51, 2008.
-
(2008)
Gene
, vol.422
, Issue.1-2
, pp. 47-51
-
-
Wol, K.1
Vendruscolo, M.2
Porto, M.3
-
7
-
-
77951235704
-
Stochastic reconstruction of protein structures from e®ective connectivity proles
-
Wol K, Vendruscolo K, Porto M, Stochastic reconstruction of protein structures from e®ective connectivity proles, PMC Biophys 26(1):5, 2008.
-
(2008)
PMC Biophys.
, vol.26
, Issue.1
, pp. 5
-
-
Wol, K.1
Vendruscolo, K.2
Porto, M.3
-
8
-
-
3142558004
-
Reconstruction of protein structures from a vectorial representation
-
Porto M, Bastolla U, Roman HE, Vendruscolo M, Reconstruction of protein structures from a vectorial representation, Phys Rev Lett 92(21):218101, 2004.
-
(2004)
Phys. Rev. Lett.
, vol.92
, Issue.21
, pp. 218101
-
-
Porto, M.1
Bastolla, U.2
Roman, H.E.3
Vendruscolo, M.4
-
9
-
-
10844225367
-
Principal eigenvector of contact matrices and hydrophobicity proles in proteins
-
Bastolla U, Porto M, Roman HE, Vendruscolo M, Principal eigenvector of contact matrices and hydrophobicity proles in proteins, Proteins: Struct Funct Bioinf 58(1):22-30, 2005.
-
(2005)
Proteins: Struct. Funct. Bioinf.
, vol.58
, Issue.1
, pp. 22-30
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
10
-
-
39849110127
-
SABERTOOTH: Protein structural alignment based on a vectorial structure representation
-
Teichert F, Bastolla U, Porto M, SABERTOOTH: Protein structural alignment based on a vectorial structure representation, BMC Bioinf 8(425):1-17, 2005.
-
(2005)
BMC Bioinf.
, vol.8
, Issue.425
, pp. 1-17
-
-
Teichert, F.1
Bastolla, U.2
Porto, M.3
-
11
-
-
77449159842
-
Efficient identication of near-native conformations in ab initio protein structure prediction using structural proles
-
Wol® K, Vendruscolo M, Porto M, Efficient identication of near-native conformations in ab initio protein structure prediction using structural proles, Proteins: Struct Funct Bioinf 78(2):249-258, 2010.
-
(2010)
Proteins: Struct. Funct. Bioinf.
, vol.78
, Issue.2
, pp. 249-258
-
-
Wol, K.1
Vendruscolo, M.2
Porto, M.3
-
12
-
-
68149125150
-
Multiscale characterization of protein conformational ensembles
-
Shehu A, Kavraki LE, Clementi C, Multiscale characterization of protein conformational ensembles, Proteins: Struct Funct Bioinf 76(4):837-851, 2009.
-
(2009)
Proteins: Struct. Funct. Bioinf.
, vol.76
, Issue.4
, pp. 837-851
-
-
Shehu, A.1
Kavraki, L.E.2
Clementi, C.3
-
13
-
-
84888711909
-
Conformational search for the protein native state
-
in Rangwala H, Karypis G, (eds Chap. 21, Wiley Book Series on Bioinformatics, Fairfax, VA
-
Shehu A, Conformational search for the protein native state, in Rangwala H, Karypis G, (eds), Protein Structure Prediction: Method and Algorithms, Chap. 21, Wiley Book Series on Bioinformatics, Fairfax, VA, 2010.
-
(2010)
Protein Structure Prediction: Method and Algorithms
-
-
Shehu, A.1
-
14
-
-
79959253922
-
In search of the protein native state with a probabilistic sampling approach
-
Olson B, Molloy K, Shehu A, In search of the protein native state with a probabilistic sampling approach, J Bioinf Comp Biol 9(3):383-398, 2011.
-
(2011)
J. Bioinf. Comp. Biol.
, vol.9
, Issue.3
, pp. 383-398
-
-
Olson, B.1
Molloy, K.2
Shehu, A.3
-
15
-
-
77954063582
-
Guiding the search for native-like protein conformations with an ab initio tree-based exploration
-
Shehu A, Olson B, Guiding the search for native-like protein conformations with an ab initio tree-based exploration, Int J Robot Res 29(8):1106-11227, 2010.
-
(2010)
Int. J. Robot. Res.
, vol.29
, Issue.8
, pp. 1106-11227
-
-
Shehu, A.1
Olson, B.2
-
16
-
-
79959375397
-
An ab initio tree-based exploration to enhance sampling of low-energy protein conformations
-
Seattle, WA, USA
-
Shehu A, An ab initio tree-based exploration to enhance sampling of low-energy protein conformations, Robot: Sci Sys, Seattle, WA, USA, pp. 241-248, 2009.
-
(2009)
Robot: Sci Sys
, pp. 241-248
-
-
Shehu, A.1
-
17
-
-
34547260921
-
Ultrafast shape recognition to search compound databases for similar molecular shapes
-
Ballester PJ, Richards G, Ultrafast shape recognition to search compound databases for similar molecular shapes, J Comput Chem 28(10):1711-1723, 2007.
-
(2007)
J. Comput. Chem.
, vol.28
, Issue.10
, pp. 1711-1723
-
-
Ballester, P.J.1
Richards, G.2
-
18
-
-
45449097303
-
Protein structure prediction using basin-hopping
-
Prentiss MC, Wales DJ, Wolynes PG, Protein structure prediction using basin-hopping, J Chem Phys 128(22):225106, 2008.
-
(2008)
J. Chem. Phys.
, vol.128
, Issue.22
, pp. 225106
-
-
Prentiss, M.C.1
Wales, D.J.2
Wolynes, P.G.3
-
20
-
-
33745610096
-
A two-stage approach for improved prediction of residue contact maps
-
Vullo A, Walsh I, Pollastri G, A two-stage approach for improved prediction of residue contact maps, BMC Bioinf 7:180, 2006.
-
(2006)
BMC Bioinf.
, vol.7
, pp. 180
-
-
Vullo, A.1
Walsh, I.2
Pollastri, G.3
-
21
-
-
33749357045
-
Crnpred: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
-
Kinjo R, Nishikawa K, CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks, BMC Bioinf 7:401, 2006.
-
(2006)
BMC Bioinf.
, vol.7
, pp. 401
-
-
Kinjo, R.1
Nishikawa, K.2
-
22
-
-
58149292218
-
Eective connectivity prole: A structural representation that evidences the relationship between protein structures and sequences
-
Bastolla U, Ortiz AR, Porto M, Teichert F, E®ective connectivity prole: A structural representation that evidences the relationship between protein structures and sequences, Proteins: Struct Funct Bioinf 73(4):872-888, 2008.
-
(2008)
Proteins: Struct. Funct. Bioinf.
, vol.73
, Issue.4
, pp. 872-888
-
-
Bastolla, U.1
Ortiz, A.R.2
Porto, M.3
Teichert, F.4
-
23
-
-
33845512710
-
Vectorial representation of single- and multi-domain protein folds
-
Teichert F, Porto M, Vectorial representation of single- and multi-domain protein folds, Eur Phys J B 54:131-136, 2006.
-
(2006)
Eur. Phys. J. B.
, vol.54
, pp. 131-136
-
-
Teichert, F.1
Porto, M.2
-
24
-
-
33748925566
-
A protein evolution model with independent sites that reproduces site-specic amino acid distributions from the protein data bank
-
Bastolla U, Porto M, Roman HE, Vendruscolo M, A protein evolution model with independent sites that reproduces site-specic amino acid distributions from the protein data bank, BMC Evol Biol 6:43, 2006.
-
(2006)
BMC Evol. Biol.
, vol.6
, pp. 43
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
25
-
-
1542618345
-
Water in protein structure prediction
-
Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG, Water in protein structure prediction, Proc. Natl. Acad. Sci. USA 101(10):3352-3357, 2004.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, Issue.10
, pp. 3352-3357
-
-
Papoian, G.A.1
Ulander, J.2
Eastwood, M.P.3
Luthey-Schulten, Z.4
Wolynes, P.G.5
-
26
-
-
70349317510
-
Restriction vs. guidance: Fragment assembly and associative memory hamiltonians for protein structure prediction
-
Hegler JA, Laetzer J, Shehu A, Clementi C, Wolynes PG, Restriction vs. guidance: Fragment assembly and associative memory hamiltonians for protein structure prediction, Proc. Natl. Acad. Sci. USA 106(36):15302-15307, 2009.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, Issue.36
, pp. 15302-15307
-
-
Hegler, J.A.1
Laetzer, J.2
Shehu, A.3
Clementi, C.4
Wolynes, P.G.5
-
27
-
-
0345059376
-
Announcing the worldwide protein data bank
-
Berman HM, Henrick K, Nakamura H, Announcing the worldwide Protein Data Bank, Nat Struct Biol 10(12):980-980, 2003.
-
(2003)
Nat. Struct. Biol.
, vol.10
, Issue.12
, pp. 980-980
-
-
Berman, H.M.1
Henrick, K.2
Nakamura, H.3
-
28
-
-
0001944742
-
Similarity search in high dimensions via hashing
-
VLDB '99 Morgan Kaufmann Publishers Inc., San Francisco, CA, USA
-
Gionis A, Indyk P, Motwani R, Similarity search in high dimensions via hashing, Intl Conf on Very Large Databases VLDB '99, Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, pp. 518-529, 1999.
-
(1999)
Intl Conf on Very Large Databases
, pp. 518-529
-
-
Gionis, A.1
Indyk, P.2
Motwani, R.3
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