ArticleJournal of chemical theory and computation2015
Energy Minimization on Manifolds for Docking Flexible Molecules.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- The Influence of Hydroxyl Group on Nerve Excitability Blockade by Limonene and Its Hydroxylated Metabolites, Perillyl Alcohol and Carveol.Molecules (Basel, Switzerland) · 2026Article
- Targeting Nudix Hydrolase 5 with Bioactive Flavonoids: Molecular Dynamics and Docking Studies for Breast Cancer Therapy.Cell biochemistry and biophysics · 2025Article
- Virtual Screening, Molecular Docking and Molecular Dynamics Simulation of Bioactive Compounds from Various Indonesian Medicinal Plants as Potential Inhibitors of Human Papillomavirus Type 16 E6 Protein in Cervical Cancer Development.Tropical life sciences research · 2025Article
- Regulation of NS5B Polymerase Activity of Hepatitis C Virus by Target Specific Phytotherapeutics: An In-Silico Molecular Dynamics Approach.Cell biochemistry and biophysics · 2024Article
- Elucidating Chiral Resolution of Aromatic Amino Acids Using Glycopeptide Selectors: A Combined Molecular Docking and Chromatographic Study.International journal of molecular sciences · 2024Article
- Baicalein analogues as prospective SARS-CoV-2 main protease (MData in brief · 2024Article
- In Silico, In Vitro, and In Vivo Evaluation of Caffeine-Coated Nanoparticles as a Promising Therapeutic Avenue for AML through NF-Kappa B and TRAIL Pathways Modulation.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Molecular Mechanisms ofPharmaceutics · 2022Article
- Improved cluster ranking in protein-protein docking using a regression approach.Computational and structural biotechnology journal · 2021Article
- Retention of antibiotic activity against resistant bacteria harbouring aminoglycoside-N-acetyltransferase enzyme by adjuvants: a combination of in-silico and in-vitro study.Scientific reports · 2020Article
- Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking.Journal of chemical theory and computation · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Discovery of a Ruthenium Complex for the Theranosis of Glioma through Targeting the Mitochondrial DNA with Bioinformatic Methods.International journal of molecular sciences · 2019Article
- Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.Journal of computer-aided molecular design · 2019Article
- Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes.Scientific reports · 2018Article
- KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking.Journal of cheminformatics · 2018Article
- Enantiomeric Resolution and Docking Studies of Chiral Xanthonic Derivatives on Chirobiotic Columns.Molecules (Basel, Switzerland) · 2018Article
- Protein-ligand docking using FFT based sampling: D3R case study.Journal of computer-aided molecular design · 2018Article
- Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors.International journal of molecular sciences · 2017Article
- New additions to the ClusPro server motivated by CAPRI.Proteins · 2017Article
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9 authors.
Funding
Abstract
In this paper, we extend a recently introduced rigid body minimization algorithm, defined on manifolds, to the problem of minimizing the energy of interacting flexible molecules. The goal is to integrate moving the ligand in six dimensional rotational/translational space with internal rotations around rotatable bonds within the two molecules. We show that adding rotational degrees of freedom to the rigid moves of the ligand results in an overall optimization search space that is a manifold to which our manifold optimization approach can be extended. The effectiveness of the method is shown for three different docking problems of increasing complexity. First, we minimize the energy of fragment-size ligands with a single rotatable bond as part of a protein mapping method developed for the identification of binding hot spots. Second, we consider energy minimization for docking a flexible ligand to a rigid protein receptor, an approach frequently used in existing methods. In the third problem, we account for flexibility in both the ligand and the receptor. Results show that minimization using the manifold optimization algorithm is substantially more efficient than minimization using a traditional all-atom optimization algorithm while producing solutions of comparable quality. In addition to the specific problems considered, the method is general enough to be used in a large class of applications such as docking multidomain proteins with flexible hinges. The code is available under open source license (at http://cluspro.bu.edu/Code/Code_Rigtree.tar) and with minimal effort can be incorporated into any molecular modeling package.
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