Concepedia

Structure-based Models

Structure-Based Models is a computational modeling framework in multiscale biomolecular modeling that derives its potential energy function predominantly from the three-dimensional structure of biomolecules, with the differentia that it simplifies molecular interactions by assuming the native structure represents the global energy minimum, thereby enabling efficient simulation of conformational dynamics and folding pathways.

1.5K

Publications

154K

Citations

5.8K

Authors

1.6K

Institutions

Publications per year

2017–2026

397

Variants

Sbms

Parents

Publications

1.5K

Scalable molecular dynamics with NAMD

J. C. Phillips, Rosemary Braun, Wei Wang et al. · Journal of Computational Chemistry · 2005 · 17.4K citations · Full text

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<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson et al. · Journal of Computational Chemistry · 1983 · 14.9K citations

, , +13

The Amber biomolecular simulation programs

David A. Case, Thomas E. Cheatham, Tom Darden et al. · Journal of Computational Chemistry · 2005 · 9.6K citations · Full text

, , +17

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

Junmei Wang, Piotr Cieplak, Peter A. Kollman · Journal of Computational Chemistry · 2000 · 4K citations

, , +17

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

David A. Pearlman, David A. Case, James W. Caldwell et al. · Computer Physics Communications · 1995 · 3.1K citations

, , +17

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Authors

5.8K

  1. DB
    David Baker

    University of Washington, United States

    13 publications · 4.6K citations

    13

    h-index

  2. WF
    Wilfred F. van Gunsteren

    ETH Zurich, Switzerland

    11 publications · 957 citations

    11

    h-index

  3. PA
    Peter A. Kollman

    University of California, San Francisco, United States

    9 publications · 8.9K citations

    9

    h-index

  4. AŠ
    Andrej Šali

    University of California, San Francisco, United States

    9 publications · 1.8K citations

    9

    h-index

  5. CL
    Charles L. Brooks

    University of Michigan, United States

    8 publications · 1.3K citations

    8

    h-index

1–5 of 5.8K

Institutions

1.6K

  1. Centre National de la Recherche Scientifique

    Paris, France

    28 h-index

    152 publications

    26.9K citations

  2. University of California, San Francisco

    San Francisco, United States

    26 h-index

    96 publications

    42.3K citations

  3. Scripps Research Institute

    San Diego, United States

    24 h-index

    83 publications

    38.6K citations

  4. National Institutes of Health

    Bethesda, United States

    21 h-index

    123 publications

    59.9K citations

  5. Howard Hughes Medical Institute

    Chevy Chase, United States

    18 h-index

    40 publications

    8.4K citations

  6. Chinese Academy of Sciences

    Beijing, China

    17 h-index

    56 publications

    2.4K citations

  7. University of Oxford

    Oxford, United Kingdom

    16 h-index

    55 publications

    2.4K citations

  8. University of California San Diego

    San Diego, United States

    16 h-index

    51 publications

    11.4K citations

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Venues

  1. Journal of Computational Chemistry

    55 publications · 54.4K citations

    33

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  2. The Journal of Chemical Physics

    55 publications · 6.9K citations

    30

    h-index

  3. Journal of Chemical Theory and Computation

    JCTC · 50 publications · 6.7K citations

    29

    h-index

  4. The Journal of Physical Chemistry B

    49 publications · 4.2K citations

    28

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  5. Journal of Chemical Information and Modeling

    JCIM · 57 publications · 2.5K citations

    28

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