Thom Vreven
Thom Vreven
Visterra, Inc.
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ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
BG Pierce, K Wiehe, H Hwang, BH Kim, T Vreven, Z Weng
Bioinformatics 30 (12), 1771-1773, 2014
Combining quantum mechanics methods with molecular mechanics methods in ONIOM
T Vreven, KS Byun, I Komáromi, S Dapprich, JA Montgomery Jr, ...
Journal of Chemical Theory and Computation 2 (3), 815-826, 2006
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
T Vreven, K Morokuma, Ö Farkas, HB Schlegel, MJ Frisch
Journal of computational chemistry 24 (6), 760-769, 2003
On the application of the IMOMO (integrated molecular orbital+ molecular orbital) method
T Vreven, K Morokuma
Journal of Computational Chemistry 21 (16), 1419-1432, 2000
Protein–protein docking benchmark version 4.0
H Hwang, T Vreven, J Janin, Z Weng
Proteins: Structure, Function, and Bioinformatics 78 (15), 3111-3114, 2010
Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
T Vreven, IH Moal, A Vangone, BG Pierce, PL Kastritis, M Torchala, ...
Journal of molecular biology 427 (19), 3031-3041, 2015
A direct derivative MC-SCF procedure
N Yamamoto, T Vreven, MA Robb, MJ Frisch, H Bernhard Schlegel
Chemical physics letters 250 (3), 373-378, 1996
The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a …
T Vreven, B Mennucci, CO da Silva, K Morokuma, J Tomasi
The Journal of chemical physics 115, 62, 2001
UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery
F Zhang, J Wang, J Xu, Z Zhang, BS Koppetsch, N Schultz, T Vreven, ...
Cell 151 (4), 871-884, 2012
Hybrid methods: Oniom (qm: mm) and qm/mm
T Vreven, K Morokuma
Annual Reports in Computational Chemistry 2, 35-51, 2006
The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing
Z Zhang, J Wang, N Schultz, F Zhang, SS Parhad, S Tu, T Vreven, ...
Cell 157 (6), 1353-1363, 2014
Ultrafast radiationless deactivation of organic dyes: evidence for a two-state two-mode pathway in polymethine cyanines
A Sanchez-Galvez, P Hunt, MA Robb, M Olivucci, T Vreven, HB Schlegel
Journal of the American Chemical Society 122 (12), 2911-2924, 2000
Ab initio photoisomerization dynamics of a simple retinal chromophore model
T Vreven, F Bernardi, M Garavelli, M Olivucci, MA Robb, HB Schlegel
Journal of the American Chemical Society 119 (51), 12687-12688, 1997
The azulene S1 state decays via a conical intersection: a CASSCF study with MMVB dynamics
MJ Bearpark, F Bernardi, S Clifford, M Olivucci, MA Robb, BR Smith, ...
Journal of the American Chemical Society 118 (1), 169-175, 1996
Investigation of the S0 S1 excitation in bacteriorhodopsin with the ONIOM (MO: MM) hybrid method
T Vreven, K Morokuma
Theoretical Chemistry Accounts 109 (3), 125-132, 2003
Photoisomerization path for a realistic retinal chromophore model: the nonatetraeniminium cation
M Garavelli, T Vreven, P Celani, F Bernardi, MA Robb, M Olivucci
Journal of the American Chemical Society 120 (6), 1285-1288, 1998
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ...
Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016
Potential-energy surfaces for ultrafast photochemistry static and dynamic aspects
M Garavelli, F Bernardi, M Olivucci, T Vreven, P Celani, MA Robb
Faraday Discuss. 110, 51-70, 1998
Hybrid ab-initio/empirical molecular dynamics: combining the ONIOM scheme with the atom-centered density matrix propagation (ADMP) approach
N Rega, SS Iyengar, GA Voth, HB Schlegel, T Vreven, MJ Frisch
The Journal of Physical Chemistry B 108 (13), 4210-4220, 2004
Geometry optimization with QM/MM methods II: Explicit quadratic coupling
T Vreven, MJ Frisch, KN Kudin, HB Schlegel, K Morokuma
Molecular Physics 104 (5-7), 701-714, 2006
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