How much can physics do for protein design?
Abstract
Physics and physical chemistry are an important thread in computational protein design, complementary to knowledge-based tools. They provide molecular mechanics scoring functions that need little or no ad hoc parameter readjustment, methods to thoroughly sample equilibrium ensembles, and different levels of approximation for conformational flexibility. They led recently to the successful redesign of a small protein using a physics-based folded state energy. Adaptive Monte Carlo or molecular dynamics schemes were discovered where protein variants are populated as per their ligand-binding free energy or catalytic efficiency. Molecular dynamics have been used for backbone flexibility. Implicit solvent models have been refined, polarizable force fields applied, and many physical insights obtained.
How strong is the evidence?
Evidence Hub reads this as a review, done in computer models (in silico), not in people. Its evidence level is 5 of 5 (Very low · case / narrative / animal / in vitro / in silico). Case reports, narrative reviews, and animal, cell or computer-model studies give the weakest evidence for human health.
Read the paper
Related studies
- Preliminary Toxicity Analysis of 3DCRT versus IMRT on the High Dose Arm of the RTOG 0126 Prostate Cancer Trial
- Adaptive Radiotherapy for Head and Neck Cancer: Initial Clinical Outcomes from a Prospective Trial
- American Association of Physicists in Medicine Task Group 263: Standardizing Nomenclatures in Radiation Oncology
- Motion Management Strategies and Technical Issues Associated with Stereotactic Body Radiotherapy of Thoracic and Upper Abdominal Tumors: A Review from NRG Oncology
- High-dose-rate interstitial brachytherapy as a monotherapy for localized prostate cancer: treatment description and preliminary results of a phase I/II clinical trial
- Highly efficient training, refinement, and validation of a knowledge-based plan quality control system for radiotherapy clinical trials
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.