-
2
-
-
78649658931
-
The mechanism of signal transduction by twocomponent systems
-
Casino P, Rubio V, Marina A (2010) The mechanism of signal transduction by twocomponent systems. Curr Opin Struct Biol 20(6):763-771.
-
(2010)
Curr Opin Struct Biol
, vol.20
, Issue.6
, pp. 763-771
-
-
Casino, P.1
Rubio, V.2
Marina, A.3
-
3
-
-
0034035586
-
Two-component and phosphorelay signal transduction
-
Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3(2):165-170.
-
(2000)
Curr Opin Microbiol
, vol.3
, Issue.2
, pp. 165-170
-
-
Hoch, J.A.1
-
4
-
-
44449112421
-
Specificity in two-component signal transduction pathways
-
Laub MT, Goulian M (2007) Specificity in two-component signal transduction pathways. Annu Rev Genet 41:121-145.
-
(2007)
Annu Rev Genet
, vol.41
, pp. 121-145
-
-
Laub, M.T.1
Goulian, M.2
-
5
-
-
77949915674
-
Interaction fidelity in two-component signaling
-
Szurmant H, Hoch JA (2010) Interaction fidelity in two-component signaling. Curr Opin Microbiol 13(2):190-197.
-
(2010)
Curr Opin Microbiol
, vol.13
, Issue.2
, pp. 190-197
-
-
Szurmant, H.1
Hoch, J.A.2
-
6
-
-
70349795241
-
Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction
-
Casino P, Rubio V, Marina A (2009) Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction. Cell 139(2):325-336.
-
(2009)
Cell
, vol.139
, Issue.2
, pp. 325-336
-
-
Casino, P.1
Rubio, V.2
Marina, A.3
-
7
-
-
0034662751
-
A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction
-
Zapf J, Sen U, Madhusudan, Hoch JA, Varughese KI (2000) A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Structure 8 (8):851-862.
-
(2000)
Structure
, vol.8
, Issue.8
, pp. 851-862
-
-
Zapf, J.1
Sen, U.2
Madhusudan3
Hoch, J.A.4
Varughese, K.I.5
-
8
-
-
70349764676
-
Structure of PAS-linked histidine kinase and the response regulator complex
-
Yamada S, et al. (2009) Structure of PAS-linked histidine kinase and the response regulator complex. Structure 17(10):1333-1344.
-
(2009)
Structure
, vol.17
, Issue.10
, pp. 1333-1344
-
-
Yamada, S.1
-
9
-
-
33745471490
-
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state
-
Varughese KI, Tsigelny I, Zhao H (2006) The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state. J Bacteriol 188(13):4970-4977.
-
(2006)
J Bacteriol
, vol.188
, Issue.13
, pp. 4970-4977
-
-
Varughese, K.I.1
Tsigelny, I.2
Zhao, H.3
-
10
-
-
0030813090
-
Molecular recognition in signal transduction: The interaction surfaces of the Spo0F response regulator with its cognate phosphorelay proteins revealed by alanine scanning mutagenesis
-
Tzeng Y-L, Hoch JA (1997) Molecular recognition in signal transduction: The interaction surfaces of the Spo0F response regulator with its cognate phosphorelay proteins revealed by alanine scanning mutagenesis. J Mol Biol 272(2):200-212.
-
(1997)
J Mol Biol
, vol.272
, Issue.2
, pp. 200-212
-
-
Tzeng, Y.-L.1
Hoch, J.A.2
-
11
-
-
78649704332
-
Systematic dissection and trajectory-scanning mutagenesis of the molecular interface that ensures specificity of two-component signaling pathways
-
Capra EJ, et al. (2010) Systematic dissection and trajectory-scanning mutagenesis of the molecular interface that ensures specificity of two-component signaling pathways. PLoS Genet 6(11):e1001220.
-
(2010)
PLoS Genet
, vol.6
, Issue.11
-
-
Capra, E.J.1
-
12
-
-
0038529775
-
Cysteine-scanning analysis of the dimerization domain of EnvZ, an osmosensing histidine kinase
-
Qin L, Cai S, Zhu Y, Inouye M (2003) Cysteine-scanning analysis of the dimerization domain of EnvZ, an osmosensing histidine kinase. J Bacteriol 185(11):3429-3435.
-
(2003)
J Bacteriol
, vol.185
, Issue.11
, pp. 3429-3435
-
-
Qin, L.1
Cai, S.2
Zhu, Y.3
Inouye, M.4
-
13
-
-
0037447059
-
Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases
-
Li L, Shakhnovich EI, Mirny LA (2003) Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci USA 100 (8):4463-4468.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.8
, pp. 4463-4468
-
-
Li, L.1
Shakhnovich, E.I.2
Mirny, L.A.3
-
14
-
-
34447104524
-
Features of protein-protein interactions in two-component signaling deduced from genomic libraries
-
eds Melvin I. Simon BRC, Alexandrine C (Academic, New York)
-
White RA, Szurmant H, Hoch JA, Hwa T (2007) Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods in Enzymology, eds Melvin I. Simon BRC, Alexandrine C (Academic, New York), Vol 422, pp 75-101.
-
(2007)
Methods in Enzymology
, vol.422
, pp. 75-101
-
-
White, R.A.1
Szurmant, H.2
Hoch, J.A.3
Hwa, T.4
-
15
-
-
44649153450
-
Rewiring the specificity of two-component signal transduction systems
-
Skerker JM, et al. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133(6):1043-1054.
-
(2008)
Cell
, vol.133
, Issue.6
, pp. 1043-1054
-
-
Skerker, J.M.1
-
16
-
-
76049105937
-
High-resolution protein complexes from integrating genomic information with molecular simulation
-
Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H (2009) High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci USA 106(52):22124-22129.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.52
, pp. 22124-22129
-
-
Schug, A.1
Weigt, M.2
Onuchic, J.N.3
Hwa, T.4
Szurmant, H.5
-
17
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 106(1):67-72.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.1
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
18
-
-
77949916106
-
Inference of direct residue contacts in two-component signaling
-
eds Melvin IS, Brian RC, Alexandrine C. Academic, New York
-
Lunt B, et al. (2010) Inference of direct residue contacts in two-component signaling. Methods in Enzymology, eds Melvin IS, Brian RC, Alexandrine C (Academic, New York), Vol 471, pp 17-41.
-
(2010)
Methods in Enzymology
, vol.471
, pp. 17-41
-
-
Lunt, B.1
-
19
-
-
39149114704
-
Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
-
Burger L, van Nimwegen E (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol 4:165.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 165
-
-
Burger, L.1
Van Nimwegen, E.2
-
20
-
-
84873424808
-
Statistical analyses of protein sequence alignments identify structures and mechanisms in signal activation of sensor histidine kinases
-
Szurmant H, Hoch JA (2013) Statistical analyses of protein sequence alignments identify structures and mechanisms in signal activation of sensor histidine kinases. Mol Microbiol 87(4):707-712.
-
(2013)
Mol Microbiol
, vol.87
, Issue.4
, pp. 707-712
-
-
Szurmant, H.1
Hoch, J.A.2
-
21
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos F, Helmer-Citterich M, Ausiello G, Valencia A (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol 271(4):511-523.
-
(1997)
J Mol Biol
, vol.271
, Issue.4
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
Valencia, A.4
-
22
-
-
0036568319
-
In silico two-hybrid system for the selection of physically interacting protein pairs
-
Pazos F, Valencia A (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47(2):219-227.
-
(2002)
Proteins
, vol.47
, Issue.2
, pp. 219-227
-
-
Pazos, F.1
Valencia, A.2
-
23
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F, et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci USA 108(49):E1293-E1301.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.49
-
-
Morcos, F.1
-
24
-
-
84862990368
-
Genomics-aided structure prediction
-
Sułkowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN (2012) Genomics-aided structure prediction. Proc Natl Acad Sci USA 109(26):10340-10345.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.26
, pp. 10340-10345
-
-
Sułkowska, J.I.1
Morcos, F.2
Weigt, M.3
Hwa, T.4
Onuchic, J.N.5
-
25
-
-
82855163967
-
Protein 3D structure computed from evolutionary sequence variation
-
Marks DS, et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS ONE 6(12):e28766.
-
(2011)
PLoS ONE
, vol.6
, Issue.12
-
-
Marks, D.S.1
-
26
-
-
84862647180
-
Three-dimensional structures of membrane proteins from genomic sequencing
-
Hopf TA, et al. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149(7):1607-1621.
-
(2012)
Cell
, vol.149
, Issue.7
, pp. 1607-1621
-
-
Hopf, T.A.1
-
27
-
-
84890816704
-
Coevolutionary signals across protein lineages help capture multiple protein conformations
-
Morcos F, Jana B, Hwa T, Onuchic JN (2013) Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci USA 110(51): 20533-20538.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.51
, pp. 20533-20538
-
-
Morcos, F.1
Jana, B.2
Hwa, T.3
Onuchic, J.N.4
-
28
-
-
84863006375
-
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis
-
Dago AE, et al. (2012) Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci USA 109(26):E1733-E1742.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.26
-
-
Dago, A.E.1
-
29
-
-
68749107059
-
Protein sectors: Evolutionary units of three-dimensional structure
-
Halabi N, Rivoire O, Leibler S, Ranganathan R (2009) Protein sectors: Evolutionary units of three-dimensional structure. Cell 138(4):774-786.
-
(2009)
Cell
, vol.138
, Issue.4
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
30
-
-
84869447010
-
Protein structure prediction from sequence variation
-
Marks DS, Hopf TA, Sander C (2012) Protein structure prediction from sequence variation. Nat Biotechnol 30(11):1072-1080.
-
(2012)
Nat Biotechnol
, vol.30
, Issue.11
, pp. 1072-1080
-
-
Marks, D.S.1
Hopf, T.A.2
Sander, C.3
-
31
-
-
84875225476
-
Emerging methods in protein co-evolution
-
de Juan D, Pazos F, Valencia A (2013) Emerging methods in protein co-evolution. Nat Rev Genet 14(4):249-261.
-
(2013)
Nat Rev Genet
, vol.14
, Issue.4
, pp. 249-261
-
-
De Juan, D.1
Pazos, F.2
Valencia, A.3
-
32
-
-
84884603324
-
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence-and structure-rich era
-
Kamisetty H, Ovchinnikov S, Baker D (2013) Assessing the utility of coevolution-based residue-residue contact predictions in a sequence-and structure-rich era. Proc Natl Acad Sci USA 110(39):15674-15679.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.39
, pp. 15674-15679
-
-
Kamisetty, H.1
Ovchinnikov, S.2
Baker, D.3
-
33
-
-
84856090271
-
PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones DT, Buchan DW, Cozzetto D, Pontil M (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2):184-190.
-
(2012)
Bioinformatics
, vol.28
, Issue.2
, pp. 184-190
-
-
Jones, D.T.1
Buchan, D.W.2
Cozzetto, D.3
Pontil, M.4
-
34
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286(5438):295-299.
-
(1999)
Science
, vol.286
, Issue.5438
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
35
-
-
84866913347
-
Correlated electrostatic mutations provide a reservoir of stability in HIV protease
-
Haq O, Andrec M, Morozov AV, Levy RM (2012) Correlated electrostatic mutations provide a reservoir of stability in HIV protease. PLoS Comput Biol 8(9):e1002675.
-
(2012)
PLoS Comput Biol
, vol.8
, Issue.9
-
-
Haq, O.1
Andrec, M.2
Morozov, A.V.3
Levy, R.M.4
-
36
-
-
79960999556
-
Coordinate linkage of HIV evolution reveals regions of immunological vulnerability
-
Dahirel V, et al. (2011) Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci USA 108(28):11530-11535.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.28
, pp. 11530-11535
-
-
Dahirel, V.1
-
37
-
-
79955792165
-
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and crosstalks
-
Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M (2011) Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS ONE 6(5):e19729.
-
(2011)
PLoS ONE
, vol.6
, Issue.5
-
-
Procaccini, A.1
Lunt, B.2
Szurmant, H.3
Hwa, T.4
Weigt, M.5
-
38
-
-
84886578448
-
The network of stabilizing contacts in proteins studied by coevolutionary data
-
Lui S, Tiana G (2013) The network of stabilizing contacts in proteins studied by coevolutionary data. J Chem Phys 139(15):155103.
-
(2013)
J Chem Phys
, vol.139
, Issue.15
, pp. 155103
-
-
Lui, S.1
Tiana, G.2
-
39
-
-
0025964291
-
Initiation of sporulation in B. Subtilis is controlled by a multicomponent phosphorelay
-
Burbulys D, Trach KA, Hoch JA (1991) Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay. Cell 64(3):545-552.
-
(1991)
Cell
, vol.64
, Issue.3
, pp. 545-552
-
-
Burbulys, D.1
Trach, K.A.2
Hoch, J.A.3
-
40
-
-
0028596145
-
Multiple protein-aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in B
-
Perego M, et al. (1994) Multiple protein-aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in B. subtilis. Cell 79(6):1047-1055.
-
(1994)
Subtilis. Cell
, vol.79
, Issue.6
, pp. 1047-1055
-
-
Perego, M.1
-
41
-
-
0033985918
-
Differential processing of propeptide inhibitors of Rap phosphatases in Bacillus subtilis
-
Jiang M, Grau R, Perego M (2000) Differential processing of propeptide inhibitors of Rap phosphatases in Bacillus subtilis. J Bacteriol 182(2):303-310.
-
(2000)
J Bacteriol
, vol.182
, Issue.2
, pp. 303-310
-
-
Jiang, M.1
Grau, R.2
Perego, M.3
-
42
-
-
34250648354
-
Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis
-
Smits WK, et al. (2007) Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis. Mol Microbiol 65(1):103-120.
-
(2007)
Mol Microbiol
, vol.65
, Issue.1
, pp. 103-120
-
-
Smits, W.K.1
-
43
-
-
0027474353
-
Multisensory activation of the phosphorelay initiating sporulation in Bacillus subtilis: Identification and sequence of the protein kinase of the alternate pathway
-
Trach KA, Hoch JA (1993) Multisensory activation of the phosphorelay initiating sporulation in Bacillus subtilis: Identification and sequence of the protein kinase of the alternate pathway. Mol Microbiol 8(1):69-79.
-
(1993)
Mol Microbiol
, vol.8
, Issue.1
, pp. 69-79
-
-
Trach, K.A.1
Hoch, J.A.2
-
44
-
-
33947411953
-
Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition
-
McLaughlin PD, et al. (2007) Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition. FEBS Lett 581(7):1425-1429.
-
(2007)
FEBS Lett
, vol.581
, Issue.7
, pp. 1425-1429
-
-
McLaughlin, P.D.1
-
45
-
-
77957111496
-
Long range dynamic effects of point-mutations trap a response regulator in an active conformation
-
Bobay BG, Thompson RJ, Hoch JA, Cavanagh J (2010) Long range dynamic effects of point-mutations trap a response regulator in an active conformation. FEBS Lett 584 (19):4203-4207.
-
(2010)
FEBS Lett
, vol.584
, Issue.19
, pp. 4203-4207
-
-
Bobay, B.G.1
Thompson, R.J.2
Hoch, J.A.3
Cavanagh, J.4
-
46
-
-
0034879819
-
Keeping signals straight in phosphorelay signal transduction
-
Hoch JA, Varughese KI (2001) Keeping signals straight in phosphorelay signal transduction. J Bacteriol 183(17):4941-4949.
-
(2001)
J Bacteriol
, vol.183
, Issue.17
, pp. 4941-4949
-
-
Hoch, J.A.1
Varughese, K.I.2
-
47
-
-
70349524998
-
Structural plasticity and catalysis regulation of a thermosensor histidine kinase
-
Albanesi D, et al. (2009) Structural plasticity and catalysis regulation of a thermosensor histidine kinase. Proc Natl Acad Sci USA 106(38):16185-16190.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.38
, pp. 16185-16190
-
-
Albanesi, D.1
-
48
-
-
0033566242
-
Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F
-
Feher VA, Cavanagh J (1999) Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F. Nature 400(6741):289-293.
-
(1999)
Nature
, vol.400
, Issue.6741
, pp. 289-293
-
-
Feher, V.A.1
Cavanagh, J.2
-
49
-
-
84872177104
-
Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid twocomponent systems
-
Townsend GE, 2nd, Raghavan V, Zwir I, Groisman EA (2013) Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid twocomponent systems. Proc Natl Acad Sci USA 110(2):E161-E169.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.2
-
-
Townsend, I.I.G.E.1
Raghavan, V.2
Zwir, I.3
Groisman, E.A.4
-
50
-
-
14244266086
-
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
-
Pandey DP, Gerdes K (2005) Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 33(3):966-976.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.3
, pp. 966-976
-
-
Pandey, D.P.1
Gerdes, K.2
-
51
-
-
0346555269
-
Optimization of specificity in a cellular protein interaction network by negative selection
-
Zarrinpar A, Park S-H, Lim WA (2003) Optimization of specificity in a cellular protein interaction network by negative selection. Nature 426(6967):676-680.
-
(2003)
Nature
, vol.426
, Issue.6967
, pp. 676-680
-
-
Zarrinpar, A.1
Park, S.-H.2
Lim, W.A.3
-
52
-
-
84858077472
-
The Pfam protein families database
-
Punta M, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40(Database issue, D1):D290-D301.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE D1
-
-
Punta, M.1
-
53
-
-
84874724662
-
Update on activities at the Universal Protein Resource (UniProt) in 2013
-
UniProt Consortium
-
UniProt Consortium (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 41(Database issue, D1):D43-D47.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE D1
-
-
-
54
-
-
77954276842
-
SMOG@ctbp:Simplified deployment of structure-based models in GROMACS
-
Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN (2010) SMOG@ctbp:Simplified deployment of structure-based models in GROMACS. Nucleic Acids Res 38(Web Server issue):W657-W661.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.WEB SERVER ISSUE
-
-
Noel, J.K.1
Whitford, P.C.2
Sanbonmatsu, K.Y.3
Onuchic, J.N.4
-
55
-
-
63449135082
-
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
-
Whitford PC, et al. (2009) An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Proteins 75(2):430-441.
-
(2009)
Proteins
, vol.75
, Issue.2
, pp. 430-441
-
-
Whitford, P.C.1
-
56
-
-
84874791762
-
Improving ranking of models for protein complexes with side chain modeling and atomic potentials
-
Viswanath S, Ravikant DV, Elber R (2013) Improving ranking of models for protein complexes with side chain modeling and atomic potentials. Proteins 81(4):592-606.
-
(2013)
Proteins
, vol.81
, Issue.4
, pp. 592-606
-
-
Viswanath, S.1
Ravikant, D.V.2
Elber, R.3
-
57
-
-
77449134208
-
PIE-efficient filters and coarse grained potentials for unbound protein-protein docking
-
Ravikant DV, Elber R (2010) PIE-efficient filters and coarse grained potentials for unbound protein-protein docking. Proteins 78(2):400-419.
-
(2010)
Proteins
, vol.78
, Issue.2
, pp. 400-419
-
-
Ravikant, D.V.1
Elber, R.2
-
58
-
-
84869784991
-
Predictive energy landscapes for protein-protein association
-
Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG (2012) Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci USA 109(47): 19244-19249.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.47
, pp. 19244-19249
-
-
Zheng, W.1
Schafer, N.P.2
Davtyan, A.3
Papoian, G.A.4
Wolynes, P.G.5
-
59
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9(1):40.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 40
-
-
Zhang, Y.1
-
60
-
-
77954065271
-
I-TASSER: A unified platform for automated protein structure and function prediction
-
Roy A, Kucukural A, Zhang Y (2010) I-TASSER: A unified platform for automated protein structure and function prediction. Nat Protoc 5(4):725-738.
-
(2010)
Nat Protoc
, vol.5
, Issue.4
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
61
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18):3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
Mackerell, A.D.1
-
62
-
-
0242593434
-
Development and current status of the CHARMM force field for nucleic acids
-
MacKerell AD, Jr., Banavali N, Foloppe N (2000-2001) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56(4):257-265.
-
(2000)
Biopolymers
, vol.56
, Issue.4
, pp. 257-265
-
-
MacKerell Jr., A.D.1
Banavali, N.2
Foloppe, N.3
-
63
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926-935.
-
(1983)
J Chem Phys
, vol.79
, Issue.2
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
64
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel D, et al. (2005) GROMACS: Fast, flexible, and free. J Comput Chem 26 (16):1701-1718.
-
(2005)
J Comput Chem
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
|