T. Vreven

发表

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

Raphael A. G. Chaleil, Z. Weng, J. Fernández-Recio, 2015, Journal of molecular biology.

On the application of the IMOMO (integrated molecular orbital + molecular orbital) method

K. Morokuma, T. Vreven, 2000 .

Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach

G. Voth, M. Frisch, H. Schlegel, 2004 .

Binding interface prediction by combining protein–protein docking results

Z. Weng, Howook Hwang, T. Vreven, 2014, Proteins.

Integrating atom‐based and residue‐based scoring functions for protein–protein docking

Z. Weng, Howook Hwang, T. Vreven, 2011, Protein science : a publication of the Protein Society.

UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery

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

Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions

Julie C. Mitchell, Jeffrey J. Gray, Z. Weng, 2013, Proteins.

Gaussian 03, Revision E.01.

G. Scuseria, M. Frisch, G. Trucks, 2007 .

Blind prediction of interfacial water positions in CAPRI

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

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

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

Prediction of protein–protein binding free energies

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

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 .

Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase.

K. Morokuma, H. Schlegel, T. Vreven, 2002, Journal of the American Chemical Society.

Analytic second derivatives for semiempirical models based on MNDO

M. Frisch, T. Vreven, G. Scalmani, 2009 .

Performance Evaluation of the Three-Layer ONIOM Method: Case Study for a Zwitterionic Peptide.

K. Morokuma, T. Vreven, Qingfang Wang, 2006, Journal of chemical theory and computation.

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study.

K. Morokuma, M. Frisch, T. Vreven, 2006, The journal of physical chemistry. B.

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.

Link atom bond length effect in ONIOM excited state calculations.

M. Frisch, G. Trucks, T. Vreven, 2010, The Journal of chemical physics.

Oscillator Strengths in ONIOM Excited State Calculations.

M. Frisch, G. Trucks, T. Vreven, 2011, Journal of chemical theory and computation.

The application of the ONIOM hybrid method to the cycloaddition reactions of bromo-substituted 2(H)-pyran-2-ones

K. Morokuma, T. Vreven, M. Bearpark, 2009 .

On the application of the IMOMO (integrated molecular orbital + molecular orbital) method

K. Morokuma, T. Vreven, 2000, J. Comput. Chem..

Prediction of the dissociation energy of hexaphenylethane using the ONIOM(MO :MO:MO) method

K. Morokuma, T. Vreven, 2002 .

Theoretical study of the SN2 reaction of Cl−(H2O)+CH3Cl using our own N-layered integrated molecular orbital and molecular mechanics polarizable continuum model method (ONIOM, PCM)

J. Tomasi, K. Morokuma, T. Vreven, 2004 .

Modeling Photochemical [4 + 4] Cycloadditions: Conical Intersections Located with CASSCF for Butadiene + Butadiene

T. Vreven, F. Bernardi, M. Olivucci, 1997 .

Performance of ZDOCK and ZRANK in CAPRI rounds 13–19

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

A direct derivative MC-SCF procedure

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

Transition states of binap-rhodium(I)-catalyzed asymmetric hydrogenation: theoretical studies on the origin of the enantioselectivity.

K. Morokuma, T. Vreven, S. Mori, 2006, Chemistry, an Asian journal.

Application of the ONIOM method to enantioselective deprotonation in the presence of spartein

M. Frisch, T. Vreven, K. B. Wiberg, 2006 .

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

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

Getting the Most out of ONIOM: Guidelines and Pitfalls

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

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 .

Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181.

M. Frisch, T. Vreven, M. Bearpark, 2008, Journal of molecular biology.

Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method

K. Morokuma, T. Vreven, K. Morokuma, 2003 .

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

Thom Vreven, Marco Garavelli, Fernando Bernardi, 1998 .

Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects

Thom Vreven, Marco Garavelli, Fernando Bernardi, 1998 .

Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D.

T. Vreven, M. Bearpark, Susan M. Larkin, 2008, The journal of physical chemistry. A.

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

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

Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model

Thom Vreven, Marco Garavelli, Fernando Bernardi, 1997 .

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.

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

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

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.

The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing

Z. Weng, P. Zamore, Jie Wang, 2014, Cell.

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.

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.

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

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

Performance of ZDOCK and IRAD in CAPRI rounds 28–34

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

Performance of ZDOCK in CAPRI rounds 20–26

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

Exploring Angular Distance in Protein-Protein Docking Algorithms

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

Performance of ZDOCK and IRAD in CAPRI rounds 39‐45

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

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

Jeffrey J. Gray, Johnathan D. Guest, J. Jeliazkov, 2021, Structure.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Theoretical Study of the 1,2 Rearrangement of Housane Radical Cations: Key Role of a Transient Cyclopentane-1,3-diyl Intermediate

T. Vreven, M. Olivucci, M. Robb, 1999 .

Ab Initio Study of the Effect of Heteroatoms and Bulky Substituents on the Strain Energies of Cyclosilanes

K. Morokuma, T. Vreven, T. Kudo, 2003 .

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..

Lysine carboxylation in proteins: OXA‐10 β‐lactamase

H. Schlegel, T. Vreven, S. Meroueh, 2005 .

Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development

T. Vreven, Luke N. Robinson, Steven K Pregizer, 2023, Frontiers in Molecular Biosciences.

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

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

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.

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.

Modeling Proton Jumps in HY Zeolite: Effects of Acid Site Heterogeneity

M. Frisch, T. Vreven, S. Auerbach, 2007 .

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 .

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.

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

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

Density functional study of the optical rotation of glucose in aqueous solution.

T. Vreven, B. Mennucci, C. D. da Silva, 2004, The Journal of organic chemistry.

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

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

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

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

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

K. Morokuma, M. Frisch, T. Vreven, 2006, Journal of chemical theory and computation.

Computational investigation into the fluorescence of luciferin analogues

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

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 .

Blind prediction of interfacial water positions in CAPRI

Julie C. Mitchell, Jeffrey J. Gray, H. Wolfson, 2014, Proteins.

Prediction of protein–protein binding free energies

Z. Weng, B. Pierce, Howook Hwang, 2012, Protein science : a publication of the Protein Society.

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

K. Morokuma, M. Frisch, T. Vreven, 2009, Journal of chemical theory and computation.

Lysine carboxylation in proteins: OXA-10 beta-lactamase.

J. Li, H. Schlegel, T. Vreven, 2005, 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..