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1
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33750570460
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Computational protein design: A novel path to future protein drugs
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Rosenberg M., and Goldblum A. Computational protein design: A novel path to future protein drugs. Curr Pharm Design 12 (2006) 3973-3997
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(2006)
Curr Pharm Design
, vol.12
, pp. 3973-3997
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Rosenberg, M.1
Goldblum, A.2
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2
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33746592898
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Knowledge-based potentials in protein design
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Poole A.M., and Ranganathan R. Knowledge-based potentials in protein design. Curr Opin Struct Biol 16 (2006) 508-513
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(2006)
Curr Opin Struct Biol
, vol.16
, pp. 508-513
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Poole, A.M.1
Ranganathan, R.2
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3
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33746635140
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Design of protein conformational switches
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Ambroggio X.I., and Kuhlman B. Design of protein conformational switches. Curr Opin Struct Biol 16 (2006) 525-530
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(2006)
Curr Opin Struct Biol
, vol.16
, pp. 525-530
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Ambroggio, X.I.1
Kuhlman, B.2
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4
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33745185322
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Intelligent design: The de novo engineering of proteins with specified functions
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Koder R.L., and Dutton P.L. Intelligent design: The de novo engineering of proteins with specified functions. Dalton Trans 25 (2006) 3045-3051
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(2006)
Dalton Trans
, vol.25
, pp. 3045-3051
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Koder, R.L.1
Dutton, P.L.2
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5
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33646374430
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Prediction and design of macromolecular structures and interactions
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Baker D. Prediction and design of macromolecular structures and interactions. Philos T Roy Soc B 361 (2006) 459-463
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(2006)
Philos T Roy Soc B
, vol.361
, pp. 459-463
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Baker, D.1
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7
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27744498365
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Electrostatics in computational protein design
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Vizcarra C.L., and Mayo S.L. Electrostatics in computational protein design. Curr Opin Chem Biol 9 (2005) 622-626
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(2005)
Curr Opin Chem Biol
, vol.9
, pp. 622-626
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Vizcarra, C.L.1
Mayo, S.L.2
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8
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23444450226
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Semi-rational approaches to engineering enzyme activity: Combining the benefits of directed evolution and rational design
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Chica R.A., Doucet N., and Pelletier J.N. Semi-rational approaches to engineering enzyme activity: Combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 16 (2005) 378-384
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(2005)
Curr Opin Biotechnol
, vol.16
, pp. 378-384
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Chica, R.A.1
Doucet, N.2
Pelletier, J.N.3
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9
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27244460904
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Protein-DNA binding specificity predictions with structural models
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Morozov A.V., Havranek J.J., Baker D., and Siggia E.D. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 33 (2005) 5781-5798
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(2005)
Nucleic Acids Res
, vol.33
, pp. 5781-5798
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Morozov, A.V.1
Havranek, J.J.2
Baker, D.3
Siggia, E.D.4
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10
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33749030723
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Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations
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Spiegel K., DeGrado W.F., and Klein M.L. Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations. Proteins 65 (2006) 317-330
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(2006)
Proteins
, vol.65
, pp. 317-330
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Spiegel, K.1
DeGrado, W.F.2
Klein, M.L.3
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11
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17744382377
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One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations
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Marshall S.A., Vizcarra C.L., and Mayo S.L. One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Sci 14 (2005) 1293-1304
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(2005)
Protein Sci
, vol.14
, pp. 1293-1304
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Marshall, S.A.1
Vizcarra, C.L.2
Mayo, S.L.3
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12
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11244318120
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Computational protein design is a challenge for implicit solvation models
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Jaramillo A., and Wodak S.J. Computational protein design is a challenge for implicit solvation models. Biophys J 88 (2005) 156-171
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(2005)
Biophys J
, vol.88
, pp. 156-171
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Jaramillo, A.1
Wodak, S.J.2
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13
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13944256616
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A 'solvated rotamer' approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
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An orientation dependent hydrogen bonding potential describing water mediated hydrogen bonds was developed from crystallographic observations and validated through estimation of mutational affinity changes and recovery of native sequences in design. Expanded rotamers with pendent water molecules were developed and used in design studies.
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Jiang L., Kuhlman B., Kortemme T.A., and Baker D. A 'solvated rotamer' approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58 (2005) 893-904. An orientation dependent hydrogen bonding potential describing water mediated hydrogen bonds was developed from crystallographic observations and validated through estimation of mutational affinity changes and recovery of native sequences in design. Expanded rotamers with pendent water molecules were developed and used in design studies.
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(2005)
Proteins
, vol.58
, pp. 893-904
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Jiang, L.1
Kuhlman, B.2
Kortemme, T.A.3
Baker, D.4
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15
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28844499162
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Coarse-graining protein energetics in sequence variables
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Zhou F., Grigoryan G., Lustig S.R., Keating A.E., Ceder G., and Morgan D. Coarse-graining protein energetics in sequence variables. Phys Rev Lett 95 (2005) 148103
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(2005)
Phys Rev Lett
, vol.95
, pp. 148103
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Zhou, F.1
Grigoryan, G.2
Lustig, S.R.3
Keating, A.E.4
Ceder, G.5
Morgan, D.6
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16
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33745620457
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Ultra-fast evaluation of protein energies directly from sequence
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Protein design approaches generally evaluate energies of candidate sequences through their structures. Cluster expansion methods were used to directly map sequence to energy for fixed backbones after training. Applications to a coiled coil, a zinc finger, and a WW domain demonstrate the power of the approach. Interestingly, an examination of dominant expansion terms reveals important structural and energetic interactions.
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Grigoryan G., Zhou F., Lustig S.R., Ceder G., Morgan D., and Keating A.E. Ultra-fast evaluation of protein energies directly from sequence. PLoS Comput Biol 2 (2006) 551-563. Protein design approaches generally evaluate energies of candidate sequences through their structures. Cluster expansion methods were used to directly map sequence to energy for fixed backbones after training. Applications to a coiled coil, a zinc finger, and a WW domain demonstrate the power of the approach. Interestingly, an examination of dominant expansion terms reveals important structural and energetic interactions.
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(2006)
PLoS Comput Biol
, vol.2
, pp. 551-563
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Grigoryan, G.1
Zhou, F.2
Lustig, S.R.3
Ceder, G.4
Morgan, D.5
Keating, A.E.6
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17
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23844557146
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A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenylation enzyme
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An approach to protein design was developed that scores on ensemble-based estimates of free energy, and the method was applied to studying the enzyme GrsA-PheA. Wild type and a known mutant with selectivity for leucine over phenylalanine were analyzed, and design and experimental validation of new leucine specific mutants were performed.
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Lilien R.H., Stevens B.W., Anderson A.C., and Donald B.R. A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenylation enzyme. J Comput Biol 12 (2005) 740-761. An approach to protein design was developed that scores on ensemble-based estimates of free energy, and the method was applied to studying the enzyme GrsA-PheA. Wild type and a known mutant with selectivity for leucine over phenylalanine were analyzed, and design and experimental validation of new leucine specific mutants were performed.
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(2005)
J Comput Biol
, vol.12
, pp. 740-761
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Lilien, R.H.1
Stevens, B.W.2
Anderson, A.C.3
Donald, B.R.4
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18
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31944436020
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Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences
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Protein design calculations were carried out on 110 native backbones using two protocols - one using a single optimal structure for each design and the other using a structural ensemble to evaluate energetic and entropic contributions. There was relatively little difference between the sequences designed by the two methods, which led to the suggestion that conformational entropy does not play a large role in determining sequence preferences in protein design.
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Hu X.Z., and Kuhlman B. Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins 62 (2006) 739-748. Protein design calculations were carried out on 110 native backbones using two protocols - one using a single optimal structure for each design and the other using a structural ensemble to evaluate energetic and entropic contributions. There was relatively little difference between the sequences designed by the two methods, which led to the suggestion that conformational entropy does not play a large role in determining sequence preferences in protein design.
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(2006)
Proteins
, vol.62
, pp. 739-748
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Hu, X.Z.1
Kuhlman, B.2
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19
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23044445176
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Exploring the charge space of protein-protein association: A proteomic study
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Shaul Y., and Schreiber G. Exploring the charge space of protein-protein association: A proteomic study. Proteins 60 (2005) 341-352
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(2005)
Proteins
, vol.60
, pp. 341-352
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Shaul, Y.1
Schreiber, G.2
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20
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17744390877
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Action-at-a-distance interactions enhance protein binding affinity
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Joughin B.A., Green D.F., and Tidor B. Action-at-a-distance interactions enhance protein binding affinity. Protein Sci 14 (2005) 1363-1369
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(2005)
Protein Sci
, vol.14
, pp. 1363-1369
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Joughin, B.A.1
Green, D.F.2
Tidor, B.3
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21
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33646373921
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High-resolution structural validation of the computational redesign of human U1A protein
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Dobson N., Dantas G., Baker D., and Varani G. High-resolution structural validation of the computational redesign of human U1A protein. Structure 14 (2006) 847-856
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(2006)
Structure
, vol.14
, pp. 847-856
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Dobson, N.1
Dantas, G.2
Baker, D.3
Varani, G.4
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22
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33745779058
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A novel minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
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The dead-end elimination algorithm applies to rigid rotamers in discrete search space. In this work the dead-end criterion was extended to apply to continuous deformation of rotamers through reconceptualizing each rotamer as representing a continuous voxel in a local conformational space. Through computation and appropriate manipulation of minimum and maximum one- and two-body energies for and between romatmeric voxels, a new guaranteed procedure was developed and applied. The new criterion is also applicable to A* searches. The applications demonstrate that configurations removed by rigid discrete search can minimize to energies lower than the minimized discrete global minimum.
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Georgiev I., Lilien R.H., and Donald B.R. A novel minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. Lecture Notes in Computer Science. 3909 (2006) 530-545. The dead-end elimination algorithm applies to rigid rotamers in discrete search space. In this work the dead-end criterion was extended to apply to continuous deformation of rotamers through reconceptualizing each rotamer as representing a continuous voxel in a local conformational space. Through computation and appropriate manipulation of minimum and maximum one- and two-body energies for and between romatmeric voxels, a new guaranteed procedure was developed and applied. The new criterion is also applicable to A* searches. The applications demonstrate that configurations removed by rigid discrete search can minimize to energies lower than the minimized discrete global minimum.
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(2006)
Lecture Notes in Computer Science.
, vol.3909
, pp. 530-545
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Georgiev, I.1
Lilien, R.H.2
Donald, B.R.3
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23
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32144439339
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Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
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Xie W., and Sahinidis N.V. Residue-rotamer-reduction algorithm for the protein side-chain conformation problem. Bioinformatics 22 (2006) 188-194
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(2006)
Bioinformatics
, vol.22
, pp. 188-194
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Xie, W.1
Sahinidis, N.V.2
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24
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33745614865
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Dramatic performance enhancements for the FASTER optimization algorithm
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FASTER is an efficient stochastic optimizer for protein design that starts by placing the rotamer with the best one-body energy at each position and then refines the design through an iterative series of improvements that involve relaxations and perturbations. The use of a short MC simulation to create a collection of high quality starting structures and focusing relaxation steps on positions that interact strongly with perturbed positions together were found to lead to significant quality and speed enhancements (up to two orders of magnitude faster).
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Allen B.D., and Mayo S.L. Dramatic performance enhancements for the FASTER optimization algorithm. J Comput Chem 27 (2006) 1071-1075. FASTER is an efficient stochastic optimizer for protein design that starts by placing the rotamer with the best one-body energy at each position and then refines the design through an iterative series of improvements that involve relaxations and perturbations. The use of a short MC simulation to create a collection of high quality starting structures and focusing relaxation steps on positions that interact strongly with perturbed positions together were found to lead to significant quality and speed enhancements (up to two orders of magnitude faster).
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(2006)
J Comput Chem
, vol.27
, pp. 1071-1075
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Allen, B.D.1
Mayo, S.L.2
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25
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32344433456
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A search algorithm for fixed-composition protein design
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Hom G.K., and Mayo S.L. A search algorithm for fixed-composition protein design. J Comput Chem 27 (2006) 375-378
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(2006)
J Comput Chem
, vol.27
, pp. 375-378
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Hom, G.K.1
Mayo, S.L.2
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26
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10644297499
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Computational methods for protein design and protein sequence variability: biased Monte Carlo and replica exchange
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Yang X., and Saven J.G. Computational methods for protein design and protein sequence variability: biased Monte Carlo and replica exchange. Chem Phys Lett 401 (2005) 205-210
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(2005)
Chem Phys Lett
, vol.401
, pp. 205-210
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Yang, X.1
Saven, J.G.2
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27
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15744367732
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Progress in the development and application of computational methods for probabilistic protein design
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Park S., Kono H., Wang W., Boder E.T., and Saven J.G. Progress in the development and application of computational methods for probabilistic protein design. Comput Chem Eng 29 (2005) 407-421
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(2005)
Comput Chem Eng
, vol.29
, pp. 407-421
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Park, S.1
Kono, H.2
Wang, W.3
Boder, E.T.4
Saven, J.G.5
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28
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33744945756
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IPRO: An iterative computational protein library redesign and optimization procedure
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Saraf M.C., Moore G.L., Goodey N.M., Cao V.Y., Benkovic S.J., and Maranas C.D. IPRO: An iterative computational protein library redesign and optimization procedure. Biophys J 90 (2006) 4167-4180
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(2006)
Biophys J
, vol.90
, pp. 4167-4180
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Saraf, M.C.1
Moore, G.L.2
Goodey, N.M.3
Cao, V.Y.4
Benkovic, S.J.5
Maranas, C.D.6
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29
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24644472964
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Specificity versus stability in computational protein design
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The SspB adaptor protein homodimer was redesigned into a heterodimer using both a stability design protocol and an explicit specificity design. Van der Waals clashes were capped at +5 kcal/mol each to approximate conformational relaxation. The stability design did not achieve heterodimer specificity, but was more stable than wild type. The specificity design did prefer heterodimer formation, but at the cost of protein stability.
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Bolon D.N., Grant R.A., Baker T.A., and Sauer R.T. Specificity versus stability in computational protein design. Proc Natl Acad Sci USA 102 (2005) 12724-12729. The SspB adaptor protein homodimer was redesigned into a heterodimer using both a stability design protocol and an explicit specificity design. Van der Waals clashes were capped at +5 kcal/mol each to approximate conformational relaxation. The stability design did not achieve heterodimer specificity, but was more stable than wild type. The specificity design did prefer heterodimer formation, but at the cost of protein stability.
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(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12724-12729
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Bolon, D.N.1
Grant, R.A.2
Baker, T.A.3
Sauer, R.T.4
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30
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33745927413
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Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface
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The authors redesigned the colicin E7 DNase-Im7 immunity protein complex to exhibit a new hydrogen-bond network and at least a 300-fold specificity switch over one of the cognate interactions. They used both a negative and positive design strategy, and sampled rigid-body orientations mimicking the natural specificity determinant. One of 11 initial designs, from the affinity protocol, was crystallized and used as the basis for the second-round design.
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Joachimiak L.A., Kortemme T., Stoddard B.L., and Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol 361 (2006) 195-208. The authors redesigned the colicin E7 DNase-Im7 immunity protein complex to exhibit a new hydrogen-bond network and at least a 300-fold specificity switch over one of the cognate interactions. They used both a negative and positive design strategy, and sampled rigid-body orientations mimicking the natural specificity determinant. One of 11 initial designs, from the affinity protocol, was crystallized and used as the basis for the second-round design.
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(2006)
J Mol Biol
, vol.361
, pp. 195-208
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Joachimiak, L.A.1
Kortemme, T.2
Stoddard, B.L.3
Baker, D.4
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31
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33745278855
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Computational redesign of endonuclease DNA binding and cleavage specificity
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The endonuclease I-MsoI was redesigned to specifically recognize a target sequence with two base-pair changes. A disrupting base-pair change was found computationally, and then amino acids were redesigned to accommodate the new base pair. This is the first study to computationally switch endonuclease recognition specificity.
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Ashworth J., Havranek J.J., Duarte C.M., Sussman D., Monnat R.J., Stoddard B.L., and Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441 (2006) 656-659. The endonuclease I-MsoI was redesigned to specifically recognize a target sequence with two base-pair changes. A disrupting base-pair change was found computationally, and then amino acids were redesigned to accommodate the new base pair. This is the first study to computationally switch endonuclease recognition specificity.
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(2006)
Nature
, vol.441
, pp. 656-659
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Ashworth, J.1
Havranek, J.J.2
Duarte, C.M.3
Sussman, D.4
Monnat, R.J.5
Stoddard, B.L.6
Baker, D.7
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32
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13844297691
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Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure
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Ali M.H., Taylor C.M., Grigoryan G., Allen K.N., Imperiali B., and Keating A.E. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure 13 (2005) 225-234
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(2005)
Structure
, vol.13
, pp. 225-234
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Ali, M.H.1
Taylor, C.M.2
Grigoryan, G.3
Allen, K.N.4
Imperiali, B.5
Keating, A.E.6
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33
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33750058234
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Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide
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Green D.F., Dennis A.T., Fam P.S., Tidor B., and Jasanoff A. Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry 45 (2006) 12547-12559
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(2006)
Biochemistry
, vol.45
, pp. 12547-12559
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Green, D.F.1
Dennis, A.T.2
Fam, P.S.3
Tidor, B.4
Jasanoff, A.5
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34
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31944435091
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Computational design of a single amino acid sequence that can switch between two distinct protein folds
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The authors designed a single amino-acid sequence that can adopt either a zinc finger-like fold or a trimeric coiled-coil, depending upon pH or the presence of transition metals.
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Ambroggio X.I., and Kuhlman B. Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc 128 (2006) 1154-1161. The authors designed a single amino-acid sequence that can adopt either a zinc finger-like fold or a trimeric coiled-coil, depending upon pH or the presence of transition metals.
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(2006)
J Am Chem Soc
, vol.128
, pp. 1154-1161
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Ambroggio, X.I.1
Kuhlman, B.2
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35
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33646173276
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Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion
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Song G., Lazar G.A., Kortemme T., Shimaoka M., Desjarlais J.R., Baker D., and Springer T.A. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem 281 (2006) 5042-5049
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(2006)
J Biol Chem
, vol.281
, pp. 5042-5049
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Song, G.1
Lazar, G.A.2
Kortemme, T.3
Shimaoka, M.4
Desjarlais, J.R.5
Baker, D.6
Springer, T.A.7
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36
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33644949935
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Recapitulation and design of protein binding peptide structures and sequences
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Sood V.D., and Baker D. Recapitulation and design of protein binding peptide structures and sequences. J Mol Biol 357 (2006) 917-927
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(2006)
J Mol Biol
, vol.357
, pp. 917-927
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Sood, V.D.1
Baker, D.2
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37
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33646146483
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Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design
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Clark L.A., Boriack-Sjodin P.A., Eldredge J., Fitch C., Friedman B., Hanf K.J., Jarpe M., Liparoto S.F., Li Y., Lugovskoy A., et al. Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design. Protein Sci 15 (2006) 949-960
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(2006)
Protein Sci
, vol.15
, pp. 949-960
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Clark, L.A.1
Boriack-Sjodin, P.A.2
Eldredge, J.3
Fitch, C.4
Friedman, B.5
Hanf, K.J.6
Jarpe, M.7
Liparoto, S.F.8
Li, Y.9
Lugovskoy, A.10
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38
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33645218704
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Engineered antibody Fc variants with enhanced effector function
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Lazar G.A., Dang W., Karki S., Vafa O., Peng J.S., Hyun L., Chan C., Chung H.S., Eivazi A., Yoder S.C., et al. Engineered antibody Fc variants with enhanced effector function. Proc Natl Acad Sci USA 103 (2006) 4005-4010
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(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 4005-4010
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Lazar, G.A.1
Dang, W.2
Karki, S.3
Vafa, O.4
Peng, J.S.5
Hyun, L.6
Chan, C.7
Chung, H.S.8
Eivazi, A.9
Yoder, S.C.10
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39
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13444302392
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Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor
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The authors developed computational design methodology to engineer a protein that binds a specificied cofactor. They designed a four-helix bundle to bind a DPP-Fe cofactor.
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Cochran F.V., Wu S.P., Wang W., Nanda V., Saven J.G., Therien M.J., and DeGrado W.F. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J Am Chem Soc 127 (2005) 1346-1347. The authors developed computational design methodology to engineer a protein that binds a specificied cofactor. They designed a four-helix bundle to bind a DPP-Fe cofactor.
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(2005)
J Am Chem Soc
, vol.127
, pp. 1346-1347
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Cochran, F.V.1
Wu, S.P.2
Wang, W.3
Nanda, V.4
Saven, J.G.5
Therien, M.J.6
DeGrado, W.F.7
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40
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13944273682
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Design of a calcium-binding protein with desired structure in a cell adhesion molecule
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2+-binding protein with specified properties.
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2+-binding protein with specified properties.
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(2005)
J Am Chem Soc
, vol.127
, pp. 2085-2093
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Yang, W.1
Wilkins, A.L.2
Ye, Y.M.3
Liu, Z.R.4
Li, S.Y.5
Urbauer, J.L.6
Hellinga, H.W.7
Kearney, A.8
van der Merwe, P.A.9
Yang, J.J.10
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41
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22544451519
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Computational prediction of native protein ligand-binding and enzyme active site sequences
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The sequences of protein ligand-binding and enzyme active sites were predicted by optimizing binding affinity. Constraints based on known catalytic mechanism were used to capture the active sites of diverse enzymes.
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Chakrabarti R., Klibanov A.M., and Friesner R.A. Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc Natl Acad Sci USA 102 (2005) 10153-10158. The sequences of protein ligand-binding and enzyme active sites were predicted by optimizing binding affinity. Constraints based on known catalytic mechanism were used to capture the active sites of diverse enzymes.
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(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10153-10158
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