-
1
-
-
84856088973
-
Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations
-
Kumar S, Dudley J, Filipski A, Liu. L. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends Genet 2011;27:377-386.
-
(2011)
Trends Genet
, vol.27
, pp. 377-386
-
-
Kumar, S.1
Dudley, J.2
Filipski, A.3
Liu, L.4
-
2
-
-
69749093207
-
Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations
-
Kumar S, Suleski MP, Markov GJ, Lawrence S, Marco A, Filipski AJ. Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Res 2009;19:1562-1569.
-
(2009)
Genome Res
, vol.19
, pp. 1562-1569
-
-
Kumar, S.1
Suleski, M.P.2
Markov, G.J.3
Lawrence, S.4
Marco, A.5
Filipski, A.J.6
-
3
-
-
68149165614
-
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
-
Kumar P, Henikoff S, Ng. PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009;4:1073-1081.
-
(2009)
Nat Protoc
, vol.4
, pp. 1073-1081
-
-
Kumar, P.1
Henikoff, S.2
Ng, P.C.3
-
4
-
-
84866111524
-
Evolutionary diagnosis method for variants in personal exomes
-
Kumar S, Sanderford M, Gray VE, Ye J, Liu. L. Evolutionary diagnosis method for variants in personal exomes. Nat Methods 2012;9:855-856.
-
(2012)
Nat Methods
, vol.9
, pp. 855-856
-
-
Kumar, S.1
Sanderford, M.2
Gray, V.E.3
Ye, J.4
Liu, L.5
-
5
-
-
84864616473
-
Human genomic disease variants: a neutral evolutionary explanation
-
Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Genome Res 2012;22:1383-1394.
-
(2012)
Genome Res
, vol.22
, pp. 1383-1394
-
-
Dudley, J.T.1
Kim, Y.2
Liu, L.3
Markov, G.J.4
Gerold, K.5
Chen, R.6
Butte, A.J.7
Kumar, S.8
-
6
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248-249.
-
(2010)
Nat Methods
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
Kondrashov, A.S.7
Sunyaev, S.R.8
-
7
-
-
79951521614
-
Using bioinformatics to predict the functional impact of SNVs
-
Cline M, Karchin. R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics 2010;27:441-448.
-
(2010)
Bioinformatics
, vol.27
, pp. 441-448
-
-
Cline, M.1
Karchin, R.2
-
8
-
-
48249136625
-
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms
-
Cheng T, Lu Y-E, Vendruscolo M, Lio P, Blundell T. Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms. PLoS Comput Biol 2008;4:e1000135.
-
(2008)
PLoS Comput Biol
, vol.4
, pp. e1000135
-
-
Cheng, T.1
Lu, Y.-E.2
Vendruscolo, M.3
Lio, P.4
Blundell, T.5
-
9
-
-
78651230959
-
Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
-
Li Y, Wen Z, Xiao J, Yin H, Yu L, Yang L, Li M. Predicting disease-associated substitution of a single amino acid by analyzing residue interactions. BMC Bioinform 2011;12-14.
-
(2011)
BMC Bioinform
, vol.12
-
-
Li, Y.1
Wen, Z.2
Xiao, J.3
Yin, H.4
Yu, L.5
Yang, L.6
Li, M.7
-
10
-
-
84872531476
-
Prediction of phenotypes of missense mutations in human proteins from biological assemblies
-
Wei Q, Xu Q, Dunbrack. RL. Prediction of phenotypes of missense mutations in human proteins from biological assemblies. Proteins 2012;81:199-213.
-
(2012)
Proteins
, vol.81
, pp. 199-213
-
-
Wei, Q.1
Xu, Q.2
Dunbrack, R.L.3
-
11
-
-
25144523127
-
Loss of protein structure stability as a major causative factor in monogenic disease
-
Yue P, Li Z, Moult J. Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 2005;353:459-473.
-
(2005)
J Mol Biol
, vol.353
, pp. 459-473
-
-
Yue, P.1
Li, Z.2
Moult, J.3
-
12
-
-
33645764714
-
SNPs3D: candidate gene and SNP selection for association studies
-
Yue P, Melamud E, Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinform 2006;7:166.
-
(2006)
BMC Bioinform
, vol.7
, pp. 166
-
-
Yue, P.1
Melamud, E.2
Moult, J.3
-
13
-
-
77955645823
-
Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties
-
Huang T, Wang P, Ye Z-Q, Xu H, He Z, Feng K-Y, Hu L, Cui W, Wang K, Dong X, Xie L, Kong X, Cai Y, Li Y. Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties. PLoS One 2010;5:e11900.
-
(2010)
PLoS One
, vol.5
, pp. e11900
-
-
Huang, T.1
Wang, P.2
Ye, Z.-Q.3
Xu, H.4
He, Z.5
Feng, K.-Y.6
Hu, L.7
Cui, W.8
Wang, K.9
Dong, X.10
Xie, L.11
Kong, X.12
Cai, Y.13
Li, Y.14
-
14
-
-
77955199287
-
Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
-
Huang T, Shi X-H, Wang P, He Z, Feng K-Y, Hu L, Kong X, Li Y, Cai Y, Chou K-C. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 2010;5:e10972.
-
(2010)
PLoS One
, vol.5
, pp. e10972
-
-
Huang, T.1
Shi, X.-H.2
Wang, P.3
He, Z.4
Feng, K.-Y.5
Hu, L.6
Kong, X.7
Li, Y.8
Cai, Y.9
Chou, K.-C.10
-
15
-
-
34848852941
-
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations
-
Zheng W, Brooks B, Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J 2007;93:2289-2299.
-
(2007)
Biophys J
, vol.93
, pp. 2289-2299
-
-
Zheng, W.1
Brooks, B.2
Thirumalai, D.3
-
16
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang Y, Rader A, Bahar I, Jernigan R. Global ribosome motions revealed with elastic network model. J Struct Biol 2004;147:303-314.
-
(2004)
J Struct Biol
, vol.147
, pp. 303-314
-
-
Wang, Y.1
Rader, A.2
Bahar, I.3
Jernigan, R.4
-
17
-
-
64249141496
-
Comparison of molecular dynamics and superfamily spaces of protein domain deformation
-
Velazquez-Muriel J, Rueda M, Cuesta I, Pascual-Montano A, Carazo J. Comparison of molecular dynamics and superfamily spaces of protein domain deformation. BMC Struct Biol 2009;9:6-.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 6
-
-
Velazquez-Muriel, J.1
Rueda, M.2
Cuesta, I.3
Pascual-Montano, A.4
Carazo, J.5
-
18
-
-
79551689721
-
Protein dynamics and allostery: an NMR view
-
Tzeng S, Kalodimos. C. Protein dynamics and allostery: an NMR view. Curr Opin Struct Biol 2011;21:62-67.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 62-67
-
-
Tzeng, S.1
Kalodimos, C.2
-
19
-
-
84861181338
-
Dissipative electro-elastic network model of protein electrostatics
-
Martin D, Ozkan SB, Matyushov D. Dissipative electro-elastic network model of protein electrostatics. Phys Biol 2012;9:036004.
-
(2012)
Phys Biol
, vol.9
, pp. 036004
-
-
Martin, D.1
Ozkan, S.B.2
Matyushov, D.3
-
20
-
-
78049433050
-
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs
-
Liu Y, Gierasch L, Bahar I. Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Comput Biol 2010;6:e1000931.
-
(2010)
PLoS Comput Biol
, vol.6
, pp. e1000931
-
-
Liu, Y.1
Gierasch, L.2
Bahar, I.3
-
21
-
-
84861434946
-
The interface of protein structure, protein biophysics, and molecular evolution
-
Liberles D, Teichmann S, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012;21:769-785.
-
(2012)
Protein Sci
, vol.21
, pp. 769-785
-
-
Liberles, D.1
Teichmann, S.2
Bahar, I.3
Bastolla, U.4
Bloom, J.5
Bornberg-Bauer, E.6
Colwell, L.J.7
de Koning, A.P.8
Dokholyan, N.V.9
Echave, J.10
Elofsson, A.11
Gerloff, D.L.12
Goldstein, R.A.13
Grahnen, J.A.14
Holder, M.T.15
Lakner, C.16
Lartillot, N.17
Lovell, S.C.18
Naylor, G.19
Perica, T.20
Pollock, D.D.21
Pupko, T.22
Regan, L.23
Roger, A.24
Rubinstein, N.25
Shakhnovich, E.26
Sjölander, K.27
Sunyaev, S.28
Teufel, A.I.29
Thorne, J.L.30
Thornton, J.W.31
Weinreich, D.M.32
Whelan, S.33
more..
-
22
-
-
84864065499
-
Protein function and allostery: a dynamic relationship
-
Kalodimos C. Protein function and allostery: a dynamic relationship. Ann N Y Acad Sci 2012;1260:81-86.
-
(2012)
Ann N Y Acad Sci
, vol.1260
, pp. 81-86
-
-
Kalodimos, C.1
-
23
-
-
76049124264
-
Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
-
Jackson C, Foo J, Tokuriki N, Afriat L, Carr P, Kim HK, Schenk G, Tawfik DS, Ollis DL. Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase. Proc Natl Acad Sci USA 2009;106:21631-21636.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 21631-21636
-
-
Jackson, C.1
Foo, J.2
Tokuriki, N.3
Afriat, L.4
Carr, P.5
Kim, H.K.6
Schenk, G.7
Tawfik, D.S.8
Ollis, D.L.9
-
24
-
-
84861139691
-
Collective dynamics differentiates functional divergence in protein evolution
-
Glembo T, Thorpe M, Farrell D, Gerek Z, Ozkan S. Collective dynamics differentiates functional divergence in protein evolution. PLoS Comput Biol 2012;8:e1002428.
-
(2012)
PLoS Comput Biol
, vol.8
, pp. e1002428
-
-
Glembo, T.1
Thorpe, M.2
Farrell, D.3
Gerek, Z.4
Ozkan, S.5
-
25
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser E, Millet O, Labeikovsky W, Korzhnev D, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005;438:117-121.
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
27
-
-
77949400204
-
A perturbative view of protein structural variation
-
Echave J, Fernandez F. A perturbative view of protein structural variation. Proteins 2009;78:173-180.
-
(2009)
Proteins
, vol.78
, pp. 173-180
-
-
Echave, J.1
Fernandez, F.2
-
28
-
-
43549093267
-
Evolutionary divergence of protein structure: the linearly forced elastic network model
-
Echave J. Evolutionary divergence of protein structure: the linearly forced elastic network model. Chem Phys Lett 2008;457:413-416.
-
(2008)
Chem Phys Lett
, vol.457
, pp. 413-416
-
-
Echave, J.1
-
29
-
-
79953823548
-
A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
-
Bhabha G, Lee J, Ekiert D, Gam J, Wilson I, Dyson HJ, Benkovic SJ, Wright PE. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 2011;332:234-238.
-
(2011)
Science
, vol.332
, pp. 234-238
-
-
Bhabha, G.1
Lee, J.2
Ekiert, D.3
Gam, J.4
Wilson, I.5
Dyson, H.J.6
Benkovic, S.J.7
Wright, P.E.8
-
30
-
-
77952938726
-
Global dynamics of proteins: bridging between structure and function
-
Bahar I, Lezon T, Yang L, Eyal E. Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys 2010;39:23-42.
-
(2010)
Annu Rev Biophys
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.2
Yang, L.3
Eyal, E.4
-
31
-
-
84875686450
-
Structural dynamics flexibility informs function and evolution at a proteome scale
-
Gerek ZN, Kumar S, Ozkan SB. Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl 2013;6:423-433.
-
(2013)
Evol Appl
, vol.6
, pp. 423-433
-
-
Gerek, Z.N.1
Kumar, S.2
Ozkan, S.B.3
-
32
-
-
84857790275
-
Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs
-
David A, Razali R, Wass MN, Sternberg MJE. Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Hum Mutat 2012;33:359-363.
-
(2012)
Hum Mutat
, vol.33
, pp. 359-363
-
-
David, A.1
Razali, R.2
Wass, M.N.3
Sternberg, M.J.E.4
-
33
-
-
77955590137
-
Human allelic variation: perspective from protein function, structure, and evolution
-
Jordan DM, Ramensky VE, Sunyaev SR. Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol 2010;20:342-350.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 342-350
-
-
Jordan, D.M.1
Ramensky, V.E.2
Sunyaev, S.R.3
-
34
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
The 1000 Genomes Project Consortium.
-
The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1, 092 human genomes. Nature 2012;491:56-65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
35
-
-
0037903275
-
Human gene mutation database (HGMD): 2003 update
-
Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN. Human gene mutation database (HGMD): 2003 update. Hum Mutat 2003;21:577-581.
-
(2003)
Hum Mutat
, vol.21
, pp. 577-581
-
-
Stenson, P.D.1
Ball, E.V.2
Mort, M.3
Phillips, A.D.4
Shiel, J.A.5
Thomas, N.S.6
Abeysinghe, S.7
Krawczak, M.8
Cooper, D.N.9
-
36
-
-
0017411710
-
The protein data bank: a computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer Jr, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
37
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996;77:1905-1908.
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.1
-
38
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
39
-
-
80055066238
-
Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning
-
Gerek ZN, Ozkan SB. Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning. PLoS Comput Biol 2011;7:e1002154.
-
(2011)
PLoS Comput Biol
, vol.7
, pp. e1002154
-
-
Gerek, Z.N.1
Ozkan, S.B.2
-
40
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001;80:505-515.
-
(2001)
Biophys J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
41
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
42
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 2004;60:2256-2268.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
43
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007;372:774-797.
-
(2007)
J Mol Biol
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
44
-
-
33646195686
-
Detection of protein assemblies in crystals
-
Krissinel E, Henrick K. Detection of protein assemblies in crystals. Comput Life Sci LNBI 2005;3695:163-174.
-
(2005)
Comput Life Sci LNBI
, vol.3695
, pp. 163-174
-
-
Krissinel, E.1
Henrick, K.2
-
45
-
-
84959747425
-
Toward defining the course of evolution: minimum change for a specific tree topology
-
Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406-416.
-
(1971)
Syst Zool
, vol.20
, pp. 406-416
-
-
Fitch, W.M.1
-
46
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002;12:996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
47
-
-
20244367772
-
Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5′-phosphate oxidase
-
Mills P, Surtees R, Champion M, Beesley C, Dalton N, Scambler PJ, Heales SJR, Briddon A, Scheimberg I, Hoffmann GF, Zschocke J, Clayton PT. Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5′-phosphate oxidase. Hum Mol Genet 2005;14:1077-1086.
-
(2005)
Hum Mol Genet
, vol.14
, pp. 1077-1086
-
-
Mills, P.1
Surtees, R.2
Champion, M.3
Beesley, C.4
Dalton, N.5
Scambler, P.J.6
Heales, S.J.R.7
Briddon, A.8
Scheimberg, I.9
Hoffmann, G.F.10
Zschocke, J.11
Clayton, P.T.12
-
48
-
-
70349911882
-
Structural determinants of protein evolution are context-sensitive at the residue level
-
Franzosa EA, Xia Y. Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol 2009;26:2387-2395.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2387-2395
-
-
Franzosa, E.A.1
Xia, Y.2
-
49
-
-
84905228048
-
Predictor performance with stratified data and imbalanced classes
-
Stone EA. Predictor performance with stratified data and imbalanced classes. Nat Methods 2014;11:782-783.
-
(2014)
Nat Methods
, vol.11
, pp. 782-783
-
-
Stone, E.A.1
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