-
1
-
-
77956042544
-
SRC: A century of science brought to the clinic
-
Aleshin, A. and Finn, R. S. SRC: A century of science brought to the clinic. Neoplasia, 12(8):599-607, 2010.
-
(2010)
Neoplasia
, vol.12
, Issue.8
, pp. 599-607
-
-
Aleshin, A.1
Finn, R.S.2
-
2
-
-
2542420004
-
The principled design of large-scale recursive neural network architectures- DAG-RNNs and the protein structure prediction problem
-
Baldi, Pierre and Pollastri, Gianluca. The principled design of large-scale recursive neural network architectures- DAG-RNNs and the protein structure prediction problem. J. Mach, Learn. Res., 4:575-602, 2003.
-
(2003)
J. Mach, Learn. Res.
, vol.4
, pp. 575-602
-
-
Baldi, P.1
Pollastri, G.2
-
3
-
-
80053979296
-
MSMBuilder2: Modeling conformational dynamics on the picosecond to millisecond scale
-
Beauchamp, Kyle A., Bowman, Gregory R., Lane, Thomas J., Maibaum, Lutz, Haque, Imran S., and Pande, Vijay S. MSMBuilder2: Modeling conformational dynamics on the picosecond to millisecond scale. J. Chem. Theory Comput., 7(10):3412-3419, 2011.
-
(2011)
J. Chem. Theory Comput.
, vol.7
, Issue.10
, pp. 3412-3419
-
-
Beauchamp, K.A.1
Bowman, G.R.2
Lane, T.J.3
Maibaum, L.4
Haque, I.S.5
Pande, V.S.6
-
4
-
-
84859611714
-
Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements
-
Beauchamp, Kyle A., Lin, Yu-Shan, Das, Rhiju, and Pande, Vijay S. Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. J. Chem. Theory Comput., 8(4): 1409-1414, 2012.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, Issue.4
, pp. 1409-1414
-
-
Beauchamp, K.A.1
Lin, Y.-S.2
Das, R.3
Pande, V.S.4
-
5
-
-
84870182404
-
Improved coarse-graining of markov state models via explicit consideration of statistical un-certainty
-
Bowman, Gregory R. Improved coarse-graining of markov state models via explicit consideration of statistical uncertainty. J. Chem. Phys., 137( 13): 134111, 2012.
-
(2012)
J. Chem. Phys.
, vol.137
, Issue.13
, pp. 134111
-
-
Bowman, G.R.1
-
6
-
-
31444452031
-
P versus q: Structural reaction coordinates capture protein folding on smooth landscapes
-
Cho, Samuel S., Levy, Yaakov, and Wolynes, Peter G. P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes. Proc. Natl. Acad. Sci. U.S.A., 103(3):586-591, 2006.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, Issue.3
, pp. 586-591
-
-
Cho, S.S.1
Levy, Y.2
Wolynes, P.G.3
-
7
-
-
33646781937
-
Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction
-
Chu, Wei, Ghahramani, Zoubin, Podtelezhnikov, Alexei, and Wild, David L. Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction. IEEE/ACM Trans. Comput. Biol. Bioinf., 3(2):98-113, 2006.
-
(2006)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.3
, Issue.2
, pp. 98-113
-
-
Chu, W.1
Ghahramani, Z.2
Podtelezhnikov, A.3
Wild, D.L.4
-
8
-
-
84877785043
-
Deep spatio-temporal architectures and learning for protein structure prediction
-
NIPS '12
-
Di Lena, Pietro, Baldi, Pierre, and Nagata, Ken. Deep spatio-temporal architectures and learning for protein structure prediction. In Adv. Neural Inf. Process. Syst. 25, NIPS '12, pp. 521-529, 2012.
-
(2012)
Adv. Neural Inf. Process. Syst.
, vol.25
, pp. 521-529
-
-
Di Lena, P.1
Baldi, P.2
Nagata, K.3
-
9
-
-
0028929556
-
Principles of protein folding - A perspective from simple exact models
-
Dill, Ken A, Bromberg, Sarina, Yue, Kaizhi, Chan, Hue Sun, Ftebig, Klaus M, Yee, David P, and Thomas, Paul D. Principles of protein folding - A perspective from simple exact models. Protein Sci., 4(4):561-602, 1995.
-
(1995)
Protein Sci.
, vol.4
, Issue.4
, pp. 561-602
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
Chan, H.S.4
Ftebig, K.M.5
Yee, D.P.6
Thomas, P.D.7
-
10
-
-
1542784498
-
Variable selection via non- concave penalized likelihood and its oracle properties
-
Fan, Jianqing and Li, Runze. Variable selection via non- concave penalized likelihood and its oracle properties. J. Am. Stat. Assoc., 96(456): 1348-1360, 2001.
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, Issue.456
, pp. 1348-1360
-
-
Fan, J.1
Li, R.2
-
11
-
-
84872511666
-
Strategies for the selective regulation of kinases with al-losteric modulators: Exploiting exclusive structural features
-
Fang, Zhizhou, Grtter, Christian, and Rauh, Daniel. Strategies for the selective regulation of kinases with al-losteric modulators: Exploiting exclusive structural features. ACS Chem. Biol., 8(1):58-70, 2013.
-
(2013)
ACS Chem. Biol
, vol.8
, Issue.1
, pp. 58-70
-
-
Fang, Z.1
Grtter, C.2
Rauh, D.3
-
12
-
-
77956214601
-
Pairwise variable selection for high-dimensional model-based clustering
-
Guo, Jian, Levina, Elizaveta, Michailidis, George, and Zhu, Ji. Pairwise variable selection for high-dimensional model-based clustering. Biometrics, 66(3):793-804, 2010.
-
(2010)
Biometrics
, vol.66
, Issue.3
, pp. 793-804
-
-
Guo, J.1
Levina, E.2
Michailidis, G.3
Zhu, J.4
-
14
-
-
0035439412
-
An algorithmic introduction to numerical simulation of stochastic differential equations
-
Higham, Desmond J. An algorithmic introduction to numerical simulation of stochastic differential equations. SIAMRev., 43(3):525-546, 2001.
-
(2001)
SIAMRev
, vol.43
, Issue.3
, pp. 525-546
-
-
Higham, D.J.1
-
15
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, William, Dalke, Andrew, and Schulten, Klaus. VMD: Visual molecular dynamics. J. Mol. Graphics, 14 (1):33 - 38, 1996.
-
(1996)
J. Mol. Graphics
, vol.14
, Issue.1
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
16
-
-
18744371588
-
Molecular dynamics and protein function
-
Karplus, M. and Kuriyan, J. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. U.S.A., 102(19): 6679-6685, 2005.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.19
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
17
-
-
84890917722
-
Cloud-based simulations on google exacycle reveal ligand modulation of gpcr activation pathways
-
Kohlhoff, Kai J, Shukla, Diwakar, Lawrenz, Morgan, Bowman, Gregory R, Konerding, David E, Belov, Dan, Alt- man, Russ B, and Pande, Vijay S. Cloud-based simulations on Google Exacycle reveal ligand modulation of gpcr activation pathways. Nat. Chem., 6(1): 15-21, 2014.
-
(2014)
Nat. Chem.
, vol.6
, Issue.1
, pp. 15-21
-
-
Kohlhoff, K.J.1
Shukla, D.2
Lawrenz, M.3
Bowman, G.R.4
Konerding, D.E.5
Belov, D.6
Alt- Man, R.B.7
Pande, V.S.8
-
18
-
-
68049084674
-
Breaking the chains: Structure and function of the deu- biquitinases
-
Komander, David, Clague, Michael J, and Urbe, Sylvie. Breaking the chains: Structure and function of the deu- biquitinases. Nat. Rev. Mol. Cell Biol., 10(8):550-563, 2009.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, Issue.8
, pp. 550-563
-
-
Komander, D.1
Clague, M.J.2
Urbe, S.3
-
19
-
-
84873526912
-
To milliseconds and beyond: Challenges in the simulation of protein folding
-
Lane, Thomas J, Shukla, Diwakar, Beauchamp, Kyle A, and Pande, Vijay S. To milliseconds and beyond: challenges in the simulation of protein folding. Curr. Opin. Struct. Biol., 23(1):58-65, 2013.
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, Issue.1
, pp. 58-65
-
-
Lane, T.J.1
Shukla, D.2
Beauchamp, K.A.3
Pande, V.S.4
-
20
-
-
16344382372
-
Protein folding: The stepwise assembly of foldon units
-
Maity, Haripada, Maity, Mita, Krishna, Mallela M. G., Mayne, Leland, and Englander, S. Walter. Protein folding: The stepwise assembly of foldon units. Proc. Natl. Acad. Sci. U.S.A., 102(13):4741-4746, 2005.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, Issue.13
, pp. 4741-4746
-
-
Maity, H.1
Maity, M.2
Krishna, M.M.G.3
Mayne, L.4
Englander, S.W.5
-
21
-
-
85098056778
-
-
Springer Series in Operations Research and Financial Engineering. Springer, New York, 2nd edition
-
Nocedal, J. and Wright, S. Numerical Optimization. Springer Series in Operations Research and Financial Engineering. Springer, New York, 2nd edition, 2006.
-
(2006)
Numerical Optimization
-
-
Nocedal, J.1
Wright, S.2
-
22
-
-
84903361996
-
Projected and hidden markov models for calculating kinetics and metastable states of complex molecules
-
Noe, Frank, Wu, Hao, Prinz, Jan-Hendrik, and Plattner, Nuria. Projected and hidden markov models for calculating kinetics and metastable states of complex molecules. J. Chem. Phys., 139(18): 184114, 2013.
-
(2013)
J. Chem. Phys.
, vol.139
, Issue.18
, pp. 184114
-
-
Noe, F.1
Wu, H.2
Prinz, J.-H.3
Plattner, N.4
-
23
-
-
79957488000
-
Markov models of molecular kinetics: Generation and validation
-
Prinz, Jan-Hendrik, Wu, Hao, Sarich, Marco, Keller, Bettina, Senne, Martin, Held, Martin, Chodera, John D., Schutte, Christof, and Noe, Frank. Markov models of molecular kinetics: Generation and validation. J. Chem. Phys., 134( 17): 174105, 2011.
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.17
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.4
Senne, M.5
Held, M.6
Chodera, J.D.7
Schutte, C.8
Noe, F.9
-
24
-
-
0024610919
-
A tutorial on hidden markov models and selected applications in speech recognition
-
Rabiner, Lawrence R. A tutorial on hidden markov models and selected applications in speech recognition. Proc. IEEE, 77(2):257-286, 1989.
-
(1989)
Proc. IEEE
, vol.77
, Issue.2
, pp. 257-286
-
-
Rabiner, L.R.1
-
25
-
-
84870912649
-
Kinetic characterization of the critical step in HIV-1 protease maturation
-
Sadiq, S. Kashif, Noe, Frank, and De Fabritiis, Gianni. Kinetic characterization of the critical step in HIV-1 protease maturation. Proc. Natl. Acad. Sci. U.S.A., 109(50): 20449-20454, 2012.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A
, vol.109
, Issue.50
, pp. 20449-20454
-
-
Sadiq, S.K.1
Noe, F.2
De Fabritiis, G.3
-
26
-
-
35348886062
-
Anton, a special-purpose machine for molecular dynamics simulation
-
ISCA '07
-
Shaw, David E. et al. Anton, a special-purpose machine for molecular dynamics simulation. In ACM Comp. Ar. 34, ISCA '07, pp. 1-12, 2007.
-
(2007)
ACM Comp. Ar.
, vol.34
, pp. 1-12
-
-
Shaw, D.E.1
-
27
-
-
0034623787
-
Screen savers of the world unite!
-
Shirts, Michael and Pande, Vijay S. Screen savers of the world unite! Science, 290(5498): 1903-1904, 2000.
-
(2000)
Science
, vol.290
, Issue.5498
, pp. 1903-1904
-
-
Shirts, M.1
Pande, V.S.2
-
28
-
-
84919832780
-
Activation pathway of src kinase reveals intermediate states as novel targets for drug design
-
Shukla, Diwakar, Meng, Yilin, Roux, Benoit, and Pande, Vijay S. Activation pathway of Src kinase reveals intermediate states as novel targets for drug design. Nat. Commun., 5, 2014.
-
(2014)
Nat. Commun.
, vol.5
-
-
Shukla, D.1
Meng, Y.2
Roux, B.3
Pande, V.S.4
-
29
-
-
84919786791
-
-
arXiv preprint arXiv: 1206.3288
-
Sontag, David, Meltzer, Talya, Globerson, Amir, Jaakkola, Tommi S, and Weiss, Yair. Tightening LP relaxations for MAP using message passing. arXiv preprint arXiv: 1206.3288, 2012.
-
(2012)
Tightening LP Relaxations for MAP Using Message Passing
-
-
Sontag, D.1
Meltzer, T.2
Globerson, A.3
Jaakkola, T.S.4
Weiss, Y.5
-
30
-
-
12844266177
-
Sparsity and smoothness via the fused lasso
-
Tibshirani, Robert, Saunders, Michael, Rosset, Saharon, Zhu, Ji, and Knight, Keith. Sparsity and smoothness via the fused lasso. J. R. Statistic. Soc. B, 67( 1 ):91-108, 2005.
-
(2005)
J. R. Statistic. Soc. B
, vol.67
, Issue.1
, pp. 91-108
-
-
Tibshirani, R.1
Saunders, M.2
Rosset, S.3
Zhu, J.4
Knight, K.5
-
31
-
-
84864495493
-
Slow unfolded- state structuring in acyl-coa binding protein folding revealed by simulation and experiment
-
Voelz, Vincent A., Jager, Marcus, Yao, Shuhuai, Chen, Yu- jie, Zhu, Li, Waldauer, Steven A., Bowman, Gregory R., Friedrichs, Mark, Bakajin, Olgica, Lapidus, Lisa J., Weiss, Shimon, and Pande, Vijay S. Slow unfolded- state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. J. Am. Chem. Soc., 134(30): 12565-12577, 2012.
-
(2012)
J. Am. Chem. Soc.
, vol.134
, Issue.30
, pp. 12565-12577
-
-
Voelz, V.A.1
Jager, M.2
Yao, S.3
Chen, Y.-J.4
Zhu, L.5
Waldauer, S.A.6
Bowman, G.R.7
Friedrichs, M.8
Bakajin, O.9
Lapidus, L.J.10
Weiss, S.11
Pande, V.S.12
-
32
-
-
84857285809
-
Protein folding is mechanistically robust
-
Weber, Jeffrey K and Pande, Vijay S. Protein folding is mechanistically robust. Biophys. J., 102(4):859-867, 2012.
-
(2012)
Biophys. J
, vol.102
, Issue.4
, pp. 859-867
-
-
Weber, J.K.1
Pande, V.S.2
-
33
-
-
0042853244
-
Protein flexibility and computer-aided drug design
-
Wong, Chung F. and McCammon, J. Andrew. Protein flexibility and computer-aided drug design. Annu. Rev. Pharmacol. Toxicol., 43(1):31-45, 2003.
-
(2003)
Annu. Rev. Pharmacol. Toxicol.
, vol.43
, Issue.1
, pp. 31-45
-
-
Wong, C.F.1
McCammon, J.A.2
-
34
-
-
84871298878
-
Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7
-
Zhang, Yingnan, Zhou, Lijuan, Rouge, Lionel, Phillips, Aaron H, Lam, Cynthia, Liu, Peter, Sandoval, Wendy, Helgason, Elizabeth, Murray, Jeremy M, Wertz, Ingrid E, et al. Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7. Nat. Chem. Biol., 9(1):51-58, 2012.
-
(2012)
Nat. Chem. Biol.
, vol.9
, Issue.1
, pp. 51-58
-
-
Zhang, Y.1
Zhou, L.2
Rouge, L.3
Phillips, A.H.4
Lam, C.5
Liu, P.6
Sandoval, W.7
Helgason, E.8
Murray, J.M.9
Wertz, I.E.10
-
35
-
-
79958212540
-
Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time- resolved IR and two-dimensional IR signals using the markov state model approach
-
Zhuang, Wei, Cui, Raymond Z., Silva, Daniel-Adriano, and Huang, Xuhui. Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time- resolved IR and two-dimensional IR signals using the markov state model approach. J. Phys. Chem. B, 115 (18):5415-5424, 2011.
-
(2011)
J. Phys. Chem. B
, vol.115
, Issue.18
, pp. 5415-5424
-
-
Zhuang, W.1
Cui, R.Z.2
Silva, D.-A.3
Huang, X.4
|