Thom Vreven

发表

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

Zhiping Weng, Mieczyslaw Torchala, Juan Fernández-Recio, 2017, Bioinform..

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

Protein–protein docking benchmark version 4.0

Zhiping Weng, Thom Vreven, Joël Janin, 2010, Proteins.

A machine learning approach for the prediction of protein surface loop flexibility

Zhiping Weng, Thom Vreven, Kevin Wiehe, 2011, Proteins.

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction

Yang Zhang, Zhiping Weng, Thom Vreven, 2019, Bioinform..

Evaluating template-based and template-free protein-protein complex structure prediction

Zhiping Weng, Thom Vreven, Brian G. Pierce, 2014, Briefings Bioinform..

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints

Thom Vreven, Michael J. Frisch, Keiji Morokuma, 2003, J. Comput. Chem..

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes

Zhiping Weng, Thom Vreven, Brian G. Pierce, 2014, BMC Bioinformatics.

Computational investigation into the fluorescence of luciferin analogues

Thom Vreven, Stephen C. Miller, T. Vreven, 2018, J. Comput. Chem..

Performance of ZDOCK and IRAD in CAPRI rounds 39‐45

Thom Vreven, Tyler M Borrman, Sweta Vangaveti, 2020, Proteins.

Deconstructing the ONIOM Hessian: Investigating Method Combinations for Transition Structures.

Ian Kirker, Thom Vreven, Lee M Thompson, 2012, Journal of chemical theory and computation.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

Performance of ZDOCK and ZRANK in CAPRI rounds 13–19

Zhiping Weng, Thom Vreven, Jui-Hung Hung, 2010, Proteins.

Model studies of the structures, reacitivities, and reaction mechanisms of metalloenzymes

Thom Vreven, Dmitry V. Khoroshun, Djamaladdin G. Musaev, 2001, IBM J. Res. Dev..

Integrating cross-linking experiments with ab initio protein-protein docking

Zhiping Weng, Devin K Schweppe, Thom Vreven, 2018, bioRxiv.

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.

Jeffrey J. Gray, Iain H. Moal, Thom Vreven, 2020, Structure.

Integrating cross-linking experiments with ab initio protein-protein docking

Zhiping Weng, Thom Vreven, Juan D. Chavez, 2018, bioRxiv.

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

Zhiping Weng, Thom Vreven, Bong-Hyun Kim, 2014, Bioinform..

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides

Zhiping Weng, Thom Vreven, Brian G. Pierce, 2020, Bioinform..

Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.

Thom Vreven, Peng Tao, H. Schlegel, 2009, Biochemistry.

Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects

Thom Vreven, Marco Garavelli, Fernando Bernardi, 1998 .

Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model

Thom Vreven, Marco Garavelli, Fernando Bernardi, 1997 .

Performance of ZDOCK and IRAD in CAPRI rounds 28–34

Zhiping Weng, Thom Vreven, Brian G Pierce, 2017, Proteins.

The ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) method for the first singlet excited (S1) state photoisomerization path of a retinal protonated Schiff base

Thom Vreven, Keiji Morokuma, K. Morokuma, 2000 .

Transition States in a Protein Environment - ONIOM QM:MM Modeling of Isopenicillin N Synthesis.

Thom Vreven, Keiji Morokuma, Michael J Frisch, 2009, Journal of chemical theory and computation.

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree-Fock.

Thom Vreven, Michael J Frisch, M. Frisch, 2009, The Journal of chemical physics.

UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery

Zhiping Weng, Fan Zhang, Thom Vreven, 2012, Cell.

A direct derivative MC-SCF procedure

Thom Vreven, Michael A. Robb, Michael J. Frisch, 1996 .

Geometry optimization with QM/MM methods II: Explicit quadratic coupling

Thom Vreven, Michael J. Frisch, Keiji Morokuma, 2006 .

Exploring Angular Distance in Protein-Protein Docking Algorithms

Zhiping Weng, Thom Vreven, Howook Hwang, 2013, PloS one.

Modeling Proton Transfer in Zeolites: Convergence Behavior of Embedded and Constrained Cluster Calculations.

Thom Vreven, Michael J Frisch, M. Frisch, 2005, Journal of chemical theory and computation.

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

Thom Vreven, Keiji Morokuma, Michael J Frisch, 2006, Journal of chemical theory and computation.

Beyond the Continuum Approach

Modesto Orozco, Ignacio Fdez. Galván, Thom Vreven, 2007 .

Performance of ZDOCK in CAPRI rounds 20–26

Zhiping Weng, Thom Vreven, Brian G Pierce, 2013, Proteins.

Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines

Thom Vreven, Massimo Olivucci, Michael A. Robb, 2000 .

Photoisomerization Path for a Realistic Retinal Chromophore Model: The Nonatetraeniminium Cation

Thom Vreven, Marco Garavelli, Fernando Bernardi, 1998 .

Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study.

Thom Vreven, Keiji Morokuma, Rajeev Prabhakar, 2005, Biochemistry.

Cooperating Rings in cis-Stilbene Lead to an S0/S1 Conical Intersection

Thom Vreven, Michael J. Bearpark, Fernando Bernardi, 1997 .

Implementation and Benchmark Tests of the DFTB Method and Its Application in the ONIOM Method

Thom Vreven, Michael J. Frisch, Keiji Morokuma, 2009 .

Blind prediction of interfacial water positions in CAPRI

Kengo Kinoshita, Haruki Nakamura, Xiaoqin Zou, 2014, Proteins.

Prediction of protein–protein binding free energies

Zhiping Weng, Thom Vreven, Brian G Pierce, 2012, Protein science : a publication of the Protein Society.

The accurate calculation and prediction of the bond dissociation energies in a series of hydrocarbons using the IMOMO (integrated molecular orbital+molecular orbital) methods

Thom Vreven, Keiji Morokuma, K. Morokuma, 1999 .

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 merocyanine in solution

Jacopo Tomasi, Benedetta Mennucci, Thom Vreven, 2001 .

Getting the Most out of ONIOM: Guidelines and Pitfalls

Thom Vreven, Michael J. Frisch, M. Frisch, 2010 .

Chapter 3 Hybrid Methods: ONIOM(QM:MM) and QM/MM

Thom Vreven, Keiji Morokuma, K. Morokuma, 2006 .

The Azulene S1 State Decays via a Conical Intersection: A CASSCF Study with MMVB Dynamics

Thom Vreven, Michael J. Bearpark, Fernando Bernardi, 1996 .

QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework.

Thom Vreven, Krishnan Raghavachari, Michael J Frisch, 2008, The Journal of chemical physics.