Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations
نویسندگان
چکیده
منابع مشابه
Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design.
BACKGROUND Non-nucleoside inhibitors of HIV reverse transcriptase are an important component of treatment against HIV infection. Novel inhibitors are sought that increase potency against variants that contain the Tyr181Cys mutation. METHODS Molecular dynamics based free energy perturbation simulations have been run to study factors that contribute to protein-ligand binding, and the results ar...
متن کاملAnalysis of ligand binding to proteins using molecular dynamics simulations.
This work aims to explore theoretically the molecular mechanisms of ligand binding to proteins through the use of molecular dynamics simulations. The binding of sodium dodecyl sulfate (SDS) to cobra cardio toxin A3 (CTX A3) and thiourea (TOU) to lysozyme have been chosen as the two model systems. Data acquisitions were made by Gromacs software. To begin with, the collisions of ligand molecules ...
متن کاملBenzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design
Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identi...
متن کاملDesigning a new tetrapeptide to inhibit the BIR3 domain of the XIAP protein via molecular dynamics simulations
The XIAP protein is a member of apoptosis proteins family. The XIAP protein plays a central role in the inhibition of apoptosis and consists of three Baculoviral IAP Repeat domains. The BIR3 domain binds directly to the N-terminal of caspase-9 and therefore it inhibits apoptosis. N-terminal tetrapeptide region of SMAC protein can bind to BIR3, inhibit it and subsequently induce apoptosis. In th...
متن کاملComparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2019
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.9b00483