-
1
-
-
0001110699
-
On bandwidth variation in kernel estimates - A square root law
-
I.S. Abramson On bandwidth variation in kernel estimates - a square root law Ann. Stat. 10 1982 1217 1223
-
(1982)
Ann. Stat.
, vol.10
, pp. 1217-1223
-
-
Abramson, I.S.1
-
2
-
-
14244272868
-
PHENIX: Building new software for automated crystallographic structure determination
-
DOI 10.1107/S0907444902016657
-
P.D. Adams, R.W. Grosse-Kunstleve, L.W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter, and T.C. Terwilliger PHENIX: building new software for automated crystallographic structure determination Acta Crystallogr. D Biol. Crystallogr. 58 2002 1948 1954 (Pubitemid 35337293)
-
(2002)
Acta Crystallographica Section D: Biological Crystallography
, vol.58
, Issue.11
, pp. 1948-1954
-
-
Adams, P.D.1
Grosse-Kunstleve, R.W.2
Hung, L.-W.3
Ioerger, T.R.4
McCoy, A.J.5
Moriarty, N.W.6
Read, R.J.7
Sacchettini, J.C.8
Sauter, N.K.9
Terwilliger, T.C.10
-
3
-
-
44949104190
-
Differentiate, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities
-
DOI 10.1002/prot.21896
-
E.D. Amir, N. Kalisman, and C. Keasar Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities Proteins 72 2008 62 73 (Pubitemid 351809148)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.1
, pp. 62-73
-
-
Amir, E.-A.D.1
Kalisman, N.2
Keasar, C.3
-
5
-
-
0031576989
-
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
DOI 10.1006/jmbi.1997.0926
-
M.J. Bower, F.E. Cohen, and R.L. Dunbrack Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool J. Mol. Biol. 267 1997 1268 1282 (Pubitemid 27192637)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.5
, pp. 1268-1282
-
-
Bower, M.J.1
Cohen, F.E.2
Dunbrack Jr., R.L.3
-
6
-
-
24944493938
-
Biochemistry: Toward high-resolution de novo structure prediction for small proteins
-
DOI 10.1126/science.1113801
-
P. Bradley, K.M. Misura, and D. Baker Toward high-resolution de novo structure prediction for small proteins Science 309 2005 1868 1871 (Pubitemid 41325099)
-
(2005)
Science
, vol.309
, Issue.5742
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
7
-
-
84898431324
-
Variable kernel estimates of multivariate densities
-
L. Breiman, J.H. Friedman, and E. Purcell Variable kernel estimates of multivariate densities Technometrics 19 1977 135 144
-
(1977)
Technometrics
, vol.19
, pp. 135-144
-
-
Breiman, L.1
Friedman, J.H.2
Purcell, E.3
-
8
-
-
21344493897
-
Locally adaptive bandwidth choice for kernel regression-estimators
-
M. Brockmann, T. Gasser, and E. Herrmann Locally adaptive bandwidth choice for kernel regression-estimators J. Am. Stat. Assoc. 88 1993 1302 1309
-
(1993)
J. Am. Stat. Assoc.
, vol.88
, pp. 1302-1309
-
-
Brockmann, M.1
Gasser, T.2
Herrmann, E.3
-
9
-
-
0345304457
-
Computational Design and Characterization of a Monomeric Helical Dinuclear Metalloprotein
-
DOI 10.1016/j.jmb.2003.10.004
-
J.R. Calhoun, H. Kono, S. Lahr, W. Wang, W.F. DeGrado, and J.G. Saven Computational design and characterization of a monomeric helical dinuclear metalloprotein J. Mol. Biol. 334 2003 1101 1115 (Pubitemid 37485692)
-
(2003)
Journal of Molecular Biology
, vol.334
, Issue.5
, pp. 1101-1115
-
-
Calhoun, J.R.1
Kono, H.2
Lahr, S.3
Wang, W.4
DeGrado, W.F.5
Saven, J.G.6
-
10
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
DOI 10.1110/ps.03154503
-
A.A. Canutescu, A.A. Shelenkov, and R.L. Dunbrack Jr. A graph-theory algorithm for rapid protein side-chain prediction Protein Sci. 12 2003 2001 2014 (Pubitemid 37022822)
-
(2003)
Protein Science
, vol.12
, Issue.9
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack Jr., R.L.3
-
11
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
DOI 10.1126/science.278.5335.82
-
B.I. Dahiyat, and S.L. Mayo De novo protein design: fully automated sequence selection Science 278 1997 82 87 (Pubitemid 27446279)
-
(1997)
Science
, vol.278
, Issue.5335
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
12
-
-
3242886389
-
MOLPROBITY: Structure validation and all-atom contact analysis for nucleic acids and their complexes
-
I.W. Davis, L.W. Murray, J.S. Richardson, and D.C. Richardson MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Nucleic Acids Res. 32 2004 W615 W619
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Davis, I.W.1
Murray, L.W.2
Richardson, J.S.3
Richardson, D.C.4
-
13
-
-
0026589733
-
The dead-end elimination theorem and its use in protein sidechain positioning
-
J. Desmet, M. De Maeyer, B. Hazes, and I. Lasters The dead-end elimination theorem and its use in protein sidechain positioning Nature 356 1992 539 542
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
De Maeyer, M.2
Hazes, B.3
Lasters, I.4
-
14
-
-
0036667731
-
Rotamer libraries in the 21st century
-
R.L. Dunbrack Jr. Rotamer libraries in the 21st century Curr. Opin. Struct. Biol. 12 2002 431 440
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 431-440
-
-
Dunbrack Jr., R.L.1
-
15
-
-
0027160197
-
Backbone-dependent rotamer library for proteins. Application to side-chain prediction
-
DOI 10.1006/jmbi.1993.1170
-
R.L. Dunbrack Jr., and M. Karplus Backbone-dependent rotamer library for proteins. Application to side-chain prediction J. Mol. Biol. 230 1993 543 574 (Pubitemid 23161363)
-
(1993)
Journal of Molecular Biology
, vol.230
, Issue.2
, pp. 543-574
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
16
-
-
0028429178
-
Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
-
R.L. Dunbrack Jr., and M. Karplus Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains Nat. Struct. Biol. 1 1994 334 340
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 334-340
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
17
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
R.L. Dunbrack Jr., and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681 (Pubitemid 27333069)
-
(1997)
Protein Science
, vol.6
, Issue.8
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
19
-
-
45649083705
-
A simple model of backbone flexibility improves modeling of side-chain conformational variability
-
G.D. Friedland, A.J. Linares, C.A. Smith, and T. Kortemme A simple model of backbone flexibility improves modeling of side-chain conformational variability J. Mol. Biol. 380 2008 757 774
-
(2008)
J. Mol. Biol.
, vol.380
, pp. 757-774
-
-
Friedland, G.D.1
Linares, A.J.2
Smith, C.A.3
Kortemme, T.4
-
21
-
-
77954643013
-
Beyond rotamers: A generative, probabilistic model of side chains in proteins
-
T. Harder, W. Boomsma, M. Paluszewski, J. Frellsen, K.E. Johansson, and T. Hamelryck Beyond rotamers: a generative, probabilistic model of side chains in proteins BMC Bioinformatics 11 2010 306
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 306
-
-
Harder, T.1
Boomsma, W.2
Paluszewski, M.3
Frellsen, J.4
Johansson, K.E.5
Hamelryck, T.6
-
22
-
-
34250792960
-
IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models
-
DOI 10.1110/ps.062658307
-
C. Hartmann, I. Antes, and T. Lengauer IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models Protein Sci. 16 2007 1294 1307 (Pubitemid 46984864)
-
(2007)
Protein Science
, vol.16
, Issue.7
, pp. 1294-1307
-
-
Hartmann, C.1
Antes, I.2
Lengauer, T.3
-
23
-
-
60849104394
-
Autofix for backward-fit sidechains: Using MolProbity and real-space refinement to put misfits in their place
-
J.J. Headd, R.M. Immormino, D.A. Keedy, P. Emsley, D.C. Richardson, and J.S. Richardson Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place J. Struct. Funct. Genomics 10 2009 83 93
-
(2009)
J. Struct. Funct. Genomics
, vol.10
, pp. 83-93
-
-
Headd, J.J.1
Immormino, R.M.2
Keedy, D.A.3
Emsley, P.4
Richardson, D.C.5
Richardson, J.S.6
-
24
-
-
14644420979
-
The Uppsala Electron-Density Server
-
DOI 10.1107/S0907444904013253
-
G.J. Kleywegt, M.R. Harris, J.Y. Zou, T.C. Taylor, A. Wahlby, and T.A. Jones The Uppsala Electron-Density Server Acta Crystallogr. D Biol. Crystallogr. 60 2004 2240 2249 (Pubitemid 41742776)
-
(2004)
Acta Crystallographica Section D: Biological Crystallography
, vol.60
, Issue.12
, pp. 2240-2249
-
-
Kleywegt, G.J.1
Harris, M.R.2
Zou, J.-Y.3
Taylor, T.C.4
Wahlby, A.5
Jones, T.A.6
-
25
-
-
74249090260
-
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
-
E. Krieger, K. Joo, J. Lee, J. Lee, S. Raman, J. Thompson, M. Tyka, D. Baker, and K. Karplus Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8 Proteins 77 Suppl 9 2009 114 122
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, 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
-
26
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
G.G. Krivov, M.V. Shapovalov, and R.L. Dunbrack Jr. Improved prediction of protein side-chain conformations with SCWRL4 Proteins 77 2009 778 795
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack Jr., R.L.3
-
27
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
B. Kuhlman, and D. Baker Native protein sequences are close to optimal for their structures Proc. Natl. Acad. Sci. USA 97 2000 10383 10388
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
28
-
-
1342324030
-
Exploring folding free energy landscapes using computational protein design
-
DOI 10.1016/j.sbi.2004.01.002
-
B. Kuhlman, and D. Baker Exploring folding free energy landscapes using computational protein design Curr. Opin. Struct. Biol. 14 2004 89 95 (Pubitemid 38249597)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.1
, pp. 89-95
-
-
Kuhlman, B.1
Baker, D.2
-
29
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
A. Leaver-Fay, M. Tyka, S.M. Lewis, O.F. Lange, J. Thompson, R. Jacak, K. Kaufman, P.D. Renfrew, C.A. Smith, and W. Sheffler ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules Methods Enzymol. 487 2011 545 574
-
(2011)
Methods Enzymol.
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
Jacak, R.6
Kaufman, K.7
Renfrew, P.D.8
Smith, C.A.9
Sheffler, W.10
-
30
-
-
0036149564
-
Side-chain modeling with an optimized scoring function
-
DOI 10.1110/ps.24902
-
S. Liang, and N.V. Grishin Side-chain modeling with an optimized scoring function Protein Sci. 11 2002 322 331 (Pubitemid 34075795)
-
(2002)
Protein Science
, vol.11
, Issue.2
, pp. 322-331
-
-
Liang, S.1
Grishin, N.V.2
-
31
-
-
0033582329
-
Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
-
DOI 10.1073/pnas.96.2.400
-
S.C. Lovell, J.M. Word, J.S. Richardson, and D.C. Richardson Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering Proc. Natl. Acad. Sci. USA 96 1999 400 405 (Pubitemid 29061220)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.2
, pp. 400-405
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
32
-
-
0034663722
-
The penultimate rotamer library
-
DOI 10.10 02/1097-01 34(2000 0815)40:3<3 89::AID-PRO T50>3.0.CO;2-2
-
S.C. Lovell, J.M. Word, J.S. Richardson, and D.C. Richardson The penultimate rotamer library Proteins 40 2000 389 408 (Pubitemid 30624447)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.3
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
34
-
-
0034957437
-
Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure
-
DOI 10.10 02/1097-02 82(200 108)59:2<7 2::AID-BIP 1007>3.0.CO;2-S
-
J. Mendes, H.A. Nagarajaram, C.M. Soares, T.L. Blundell, and M.A. Carrondo Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure Biopolymers 59 2001 72 86 (Pubitemid 32612636)
-
(2001)
Biopolymers
, vol.59
, Issue.2
, pp. 72-86
-
-
Mendes, J.1
Nagarajaram, H.A.2
Soares, C.M.3
Blundell, T.L.4
Carrondo, M.A.5
-
35
-
-
14144256681
-
Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
-
DOI 10.1016/j.jmb.2004.12.019
-
N. Pokala, and T.M. Handel Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity J. Mol. Biol. 347 2005 203 227 (Pubitemid 40283639)
-
(2005)
Journal of Molecular Biology
, vol.347
, Issue.1
, pp. 203-227
-
-
Pokala, N.1
Handel, T.M.2
-
36
-
-
2442449534
-
Modeling Structurally Variable Regions in Homologous Proteins with Rosetta
-
DOI 10.1002/prot.10629
-
C.A. Rohl, C.E. Strauss, D. Chivian, and D. Baker Modeling structurally variable regions in homologous proteins with Rosetta Proteins 55 2004 656 677 (Pubitemid 38620090)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.3
, pp. 656-677
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Chivian, D.3
Baker, D.4
-
38
-
-
0004195611
-
-
PhD dissertation, Department of Statistics, Rice University, Houston, Texas
-
Sain, S.R. (1994). Adaptive kernel density estimation. PhD dissertation, Department of Statistics, Rice University, Houston, Texas.
-
(1994)
Adaptive Kernel Density Estimation
-
-
Sain, S.R.1
-
39
-
-
33744945756
-
IPRO: An iterative computational protein library redesign and optimization procedure
-
DOI 10.1529/biophysj.105.079277
-
M.C. Saraf, G.L. Moore, N.M. Goodey, V.Y. Cao, S.J. Benkovic, and C.D. Maranas IPRO: an iterative computational protein library redesign and optimization procedure Biophys. J. 90 2006 4167 4180 (Pubitemid 43846131)
-
(2006)
Biophysical Journal
, vol.90
, Issue.11
, pp. 4167-4180
-
-
Saraf, M.C.1
Moore, G.L.2
Goodey, N.M.3
Cao, V.Y.4
Benkovic, S.J.5
Maranas, C.D.6
-
40
-
-
33846011887
-
Statistical and conformational analysis of the electron density of protein side chains
-
DOI 10.1002/prot.21150
-
M.V. Shapovalov, and R.L. Dunbrack Jr. Statistical and conformational analysis of the electron density of protein side chains Proteins 66 2007 279 303 (Pubitemid 46053463)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.2
, pp. 279-303
-
-
Shapovalov, M.V.1
Dunbrack Jr., R.L.2
-
42
-
-
45649084560
-
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
-
C.A. Smith, and T. Kortemme Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction J. Mol. Biol. 380 2008 742 756
-
(2008)
J. Mol. Biol.
, vol.380
, pp. 742-756
-
-
Smith, C.A.1
Kortemme, T.2
-
43
-
-
34249852797
-
Andante: Reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities
-
DOI 10.1093/bioinformatics/btm073
-
R.E. Smith, S.C. Lovell, D.F. Burke, R.W. Montalvao, and T.L. Blundell Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities Bioinformatics 23 2007 1099 1105 (Pubitemid 47050561)
-
(2007)
Bioinformatics
, vol.23
, Issue.9
, pp. 1099-1105
-
-
Smith, R.E.1
Lovell, S.C.2
Burke, D.F.3
Montalvao, R.W.4
Blundell, T.L.5
-
44
-
-
79955721644
-
Structure-guided forcefield optimization
-
Y. Song, M. Tyka, A. Leaver-Fay, J. Thompson, and D. Baker Structure-guided forcefield optimization Proteins 2011 in press. Published online February 15, 2011
-
(2011)
Proteins
-
-
Song, Y.1
Tyka, M.2
Leaver-Fay, A.3
Thompson, J.4
Baker, D.5
-
45
-
-
33744490988
-
MUMBO: A protein-design approach to crystallographic model building and refinement
-
DOI 10.1107/S0907444906013333
-
M.T. Stiebritz, and Y.A. Muller MUMBO: a protein-design approach to crystallographic model building and refinement Acta Crystallogr. D Biol. Crystallogr. 62 2006 648 658 (Pubitemid 43806643)
-
(2006)
Acta Crystallographica Section D: Biological Crystallography
, vol.62
, Issue.6
, pp. 648-658
-
-
Stiebritz, M.T.1
Muller, Y.A.2
-
46
-
-
78650918983
-
Alternate states of proteins revealed by detailed energy landscape mapping
-
M.D. Tyka, D.A. Keedy, I. Andre, F. Dimaio, Y. Song, D.C. Richardson, J.S. Richardson, and D. Baker Alternate states of proteins revealed by detailed energy landscape mapping J. Mol. Biol. 405 2011 607 618
-
(2011)
J. Mol. Biol.
, vol.405
, pp. 607-618
-
-
Tyka, M.D.1
Keedy, D.A.2
Andre, I.3
Dimaio, F.4
Song, Y.5
Richardson, D.C.6
Richardson, J.S.7
Baker, D.8
-
47
-
-
23144438711
-
PISCES: Recent improvements to a PDB sequence culling server
-
G. Wang, and R.L. Dunbrack Jr. PISCES: recent improvements to a PDB sequence culling server Nucleic Acids Res. 33 2005 W94 W98
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
48
-
-
33845279881
-
Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions
-
K.B. Wiberg, and M.A. Murcko Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions J. Am. Chem. Soc. 110 1988 8029 8038
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 8029-8038
-
-
Wiberg, K.B.1
Murcko, M.A.2
-
49
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
DOI 10.1006/jmbi.1998.2401
-
J.M. Word, S.C. Lovell, J.S. Richardson, and D.C. Richardson Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285 1999 1735 1747 (Pubitemid 29060467)
-
(1999)
Journal of Molecular Biology
, vol.285
, Issue.4
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
50
-
-
1642575364
-
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
-
DOI 10.1110/ps.03411904
-
C. Zhang, S. Liu, and Y. Zhou Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential Protein Sci. 13 2004 391 399 (Pubitemid 38124960)
-
(2004)
Protein Science
, vol.13
, Issue.2
, pp. 391-399
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
|