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D-Index & Metrics

Chemistry

D-Index
57
Citations
24565
World Ranking
10910
National Ranking
2990

Overview

Woody Sherman is affiliated with Psivant Therapeutics in the United States and has contributed extensively to the field of Biochemistry, Genetics, and Molecular Biology with a focus on Molecular Biology as their primary subfield. Their research spans across Computational Theory and Mathematics, Materials Chemistry, Spectroscopy, and Immunology.

Their publication record includes significant work on topics such as Protein Structure and Dynamics, Computational Drug Discovery Methods, Enzyme Structure and Function, Machine Learning in Materials Science, Protein Degradation and Inhibitors, Ubiquitin and proteasome pathways, and Spectroscopy and Quantum Chemical Studies.

Notable recent papers by Woody Sherman include:

  • Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery, 2020, Journal of Chemical Information and Modeling
  • Rigorous Free Energy Simulations in Virtual Screening, 2020, Journal of Chemical Information and Modeling
  • Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry, 2022, Nature Communications
  • Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials, 2020, Journal of Chemical Theory and Computation
  • Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods, 2023, Journal of Chemical Information and Modeling

Frequent co-authors include Huafeng Xu, István Kolossváry, Brian K. Radak, Rafal Wiewiora, and Bryce K. Allen, reflecting collaborative work primarily within computational and biochemical research domains.

Woody Sherman's contributions have been published predominantly in the following venues:

  • Journal of Chemical Information and Modeling
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Chemical Biology & Drug Design
  • Journal of Chemical Theory and Computation
  • arXiv (Cornell University)

Best Publications

  • Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

    G. Madhavi Sastry;Matvey Adzhigirey;Tyler Day;Ramakrishna Annabhimoju

  • Novel procedure for modeling ligand/receptor induced fit effects.

    Woody Sherman;Tyler Day;Matthew P Jacobson;Richard A Friesner

  • Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

    Devleena Shivakumar;Joshua Williams;Yujie Wu;Wolfgang Damm

  • Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

    Lingle Wang;Yujie Wu;Yuqing Deng;Byungchan Kim

  • Improved Docking of Polypeptides with Glide

    Ivan Tubert-Brohman;Woody Sherman;Matthew P. Repasky;Thijs Beuming

  • Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

    Zoe Cournia;Bryce Allen;Woody Sherman

  • Use of an Induced Fit Receptor Structure in Virtual Screening

    Woody Sherman;Hege S. Beard;Ramy Farid

  • ConfGen: a conformational search method for efficient generation of bioactive conformers.

    K. Shawn Watts;Pranav Dalal;Robert B. Murphy;Woody Sherman

  • Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

    Jianxin Duan;Steven L. Dixon;Jeffrey F. Lowrie;Woody Sherman

  • Probing the alpha-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis.

    Zuojun Guo;Udayan Mohanty;Justin Noehre;Tomi K. Sawyer

  • Rational Approaches to Improving Selectivity in Drug Design

    David J. Huggins;Woody Sherman;Bruce Tidor

  • Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase.

    Phillip W. Snyder;Jasmin Mecinovic;Demetri T. Moustakas;Samuel W. Thomas

  • Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

    G. Madhavi Sastry;Jeffrey F. Lowrie;Steven L. Dixon;Woody Sherman

  • Water networks contribute to enthalpy/entropy compensation in protein-ligand binding.

    Benjamin Breiten;Matthew R. Lockett;Woody Sherman;Shuji Fujita

  • Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

    Devleena Shivakumar;Edward Harder;Wolfgang Damm;Richard A Friesner

  • Novel method for generating structure-based pharmacophores using energetic analysis.

    Noeris K. Salam;Roberto Nuti;Woody Sherman

  • Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

    Tai Sung Lee;Bryce K. Allen;Timothy J. Giese;Zhenyu Guo

  • Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes.

    Hege Beard;Anuradha Cholleti;David Pearlman;Woody Sherman

  • Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring.

    G. Madhavi Sastry;Steven L. Dixon;Woody Sherman

  • Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.

    Lingle Wang;Yuqing Deng;Jennifer L. Knight;Yujie Wu

  • Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

    Louis A. Clark;P. Ann Boriack-Sjodin;John Eldredge;Christopher Fitch

Frequent Co-Authors

Richard A. Friesner
Richard A. Friesner Columbia University
George M. Whitesides
George M. Whitesides Harvard University
Michael K. Gilson
Michael K. Gilson University of California, San Diego
F. Matthias Bickelhaupt
F. Matthias Bickelhaupt Vrije Universiteit Amsterdam
Adriaan P. IJzerman
Adriaan P. IJzerman Leiden University
Wolfgang Sippl
Wolfgang Sippl Martin Luther University Halle-Wittenberg
Lila M. Gierasch
Lila M. Gierasch University of Massachusetts Amherst
Jiri Gut
Jiri Gut University of California, San Francisco
Rebecca C. Wade
Rebecca C. Wade Heidelberg Institute for Theoretical Studies

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