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Chemistry

D-Index
43
Citations
11213
World Ranking
17049
National Ranking
4199

Overview

Thom Vreven is affiliated with Visterra in the United States and has contributed to the field of Biochemistry, Genetics, and Molecular Biology, with a research focus on Molecular Biology, Radiology, Nuclear Medicine and Imaging, Immunology, Genetics, and Computational Theory and Mathematics.

Their research spans several interconnected topics including:

  • Monoclonal and Polyclonal Antibodies Research
  • Glycosylation and Glycoproteins Research
  • Vaccines and Immunoinformatics Approaches
  • Protein Structure and Dynamics
  • Chronic Lymphocytic Leukemia Research
  • T-cell and B-cell Immunology
  • Immunotherapy and Immune Responses

Recent publications authored or co-authored by Thom Vreven include:

  • "An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants," 2021, published in Structure
  • "High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides," 2020, published in Bioinformatics
  • "An Expanded Benchmark for Antibody-Antigen Docking and Affinity Prediction Reveals Insights into Antibody Recognition Determinants," 2020, published in SSRN Electronic Journal
  • "Performance of ZDOCK and IRAD in CAPRI rounds 39-45," 2020, published in Proteins Structure Function and Bioinformatics
  • "Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development," 2023, published in Frontiers in Molecular Biosciences

Thom Vreven has collaborated frequently with researchers such as Zhiping Weng, Brian G. Pierce, Iain H. Moal, Johnathan D. Guest, and Jeliazko R. Jeliazkov.

Their work has appeared in various scientific journals, including:

  • Structure
  • Bioinformatics
  • SSRN Electronic Journal
  • Proteins Structure Function and Bioinformatics
  • Frontiers in Molecular Biosciences

Best Publications

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

    Brian G. Pierce;Kevin Wiehe;Howook Hwang;Bong-Hyun Kim

  • Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

    Thom Vreven;K Suzie Byun;István Komáromi;Stefan Dapprich

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

    Thom Vreven;Keiji Morokuma;Ödön Farkas;Ödön Farkas;H. Bernhard Schlegel

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

    Thom Vreven;Keiji Morokuma

  • Protein–protein docking benchmark version 4.0

    Howook Hwang;Thom Vreven;Joël Janin;Zhiping Weng

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

    Thom Vreven;Iain H. Moal;Anna Vangone;Brian G. Pierce

  • A direct derivative MC-SCF procedure

    Naoko Yamamoto;Thom Vreven;Michael A. Robb;Michael J. Frisch

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

    Thom Vreven;Keiji Morokuma

  • 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

    Thom Vreven;Benedetta Mennucci;Clarissa O. da Silva;Keiji Morokuma

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

    Adelaida Sanchez-Galvez;Patricia Hunt;Michael A. Robb;Massimo Olivucci

  • Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method

    T. Vreven;K. Morokuma

  • Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model

    Thom Vreven;Fernando Bernardi;Marco Garavelli;Massimo Olivucci

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

    Michael J. Bearpark;Fernando Bernardi;Simon Clifford;Massimo Olivucci

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

    Marco Garavelli;Thom Vreven;Paolo Celani;Fernando Bernardi

  • Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects

    Marco Garavelli;Fernando Bernardi;Massimo Olivucci;Thom Vreven

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

    T. Vreven;M. J. Frisch;K. N. Kudin;H. B. Schlegel

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

    Nadia Rega;Srinivasan S. Iyengar;Gregory A. Voth;H. Bernhard Schlegel

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

    Marc F. Lensink;Sameer Velankar;Andriy Kryshtafovych;Shen You Huang

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

    Sarel J. Fleishman;Sarel J. Fleishman;Timothy A. Whitehead;Eva Maria Strauch;Jacob E. Corn;Jacob E. Corn

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

    Maricel Torrent;Thom Vreven;Djamaladdin G. Musaev;Keiji Morokuma

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

    Rajeev Prabhakar;Thorn Vreven;Keiji Morokuma;Djamaladdin G. Musaev

  • 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

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

    Michael J. Bearpark;Fernando Bernardi;Simon Clifford;Massimo Olivucci

Frequent Co-Authors

Zhiping Weng
Zhiping Weng University of Massachusetts Chan Medical School
Keiji Morokuma
Keiji Morokuma Kyoto University
Massimo Olivucci
Massimo Olivucci University of Siena
Juan Fernández-Recio
Juan Fernández-Recio Spanish National Research Council
Michael A. Robb
Michael A. Robb Imperial College London
Michael J. Frisch
Michael J. Frisch Gaussian Inc.
Paul A. Bates
Paul A. Bates The Francis Crick Institute
Jeffrey J. Gray
Jeffrey J. Gray Johns Hopkins University
H. Bernhard Schlegel
H. Bernhard Schlegel Wayne State University
Shoshana J. Wodak
Shoshana J. Wodak Vrije Universiteit Brussel

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