AI Article Synopsis
- The binding energy distribution analysis method (BEDAM) was used in the SAMPL4 challenge to predict binding free energies of octa-acid host-guest complexes.
- These predictions were among the most accurate in the challenge, correlating well with unknown experimental values.
- The hands-on graduate class successfully utilized automated tools for calculations, demonstrating that even non-specialists can effectively use physics-based models for binding energy estimation.
Article Abstract
The binding energy distribution analysis method (BEDAM) protocol has been employed as part of the SAMPL4 blind challenge to predict the binding free energies of a set of octa-acid host-guest complexes. The resulting predictions were consistently judged as some of the most accurate predictions in this category of the SAMPL4 challenge in terms of quantitative accuracy and statistical correlation relative to the experimental values, which were not known at the time the predictions were made. The work has been conducted as part of a hands-on graduate class laboratory session. Collectively the students, aided by automated setup and analysis tools, performed the bulk of the calculations and the numerical and structural analysis. The success of the experiment confirms the reliability of the BEDAM methodology and it shows that physics-based atomistic binding free energy estimation models, when properly streamlined and automated, can be successfully employed by non-specialists.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832917 | PMC |
| http://dx.doi.org/10.1007/s10822-014-9795-2 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Background: Glycosylated hemoglobin (HbA1c) is a stable compound in human blood that covalently binds the N-terminal valine residue of the β-chain in hemoglobin A to the free aldehyde group of glucose. It can reflect the average blood glucose level of patients in the past 2 - 3 months. Therefore, the accuracy of HbA1c detection results is of great significance for the diagnosis and differential diagnosis of diabetes.
View Article and Find Full Text PDFUBE2S, downregulated by miR-152-3p, facilitates prostate cancer progression through the PTEN-mediated AKT/mTOR pathway.
Hum Mol Genet
January 2025
Departments of Urology, Affiliated Hospital of Chifeng University, No. 42 Wangfu Street, 024000, Chifeng, China.
Objectives: In recent years, the incidence and mortality rates of prostate cancer (PCa) have still not been significantly reduced and the mechanisms of tumor onset and progression are still not fully understood. The pathogenic mechanisms and upstream regulation of UBE2S expression in prostate cancer have not been elucidated.
Methods: Here, we performed bioinformatic analysis of public databases to reveal the expression of UBE2S in PCa and its association with Gleason score, tumor staging, biochemical recurrence, and survival.
Identification of IGFBP3 and LGALS1 as potential secreted biomarkers for clear cell renal cell carcinoma based on bioinformatics analysis and machine learning.
Adv Clin Exp Med
January 2025
Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, USA.
Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC). Due to the lack of symptoms until advanced stages, early diagnosis of ccRCC is challenging. Therefore, the identification of novel secreted biomarkers for the early detection of ccRCC is urgently needed.
View Article and Find Full Text PDFComputational exploration of palmitoyl-protein thioesterase 1 inhibition by L. for anti-dementia treatment.
J Taibah Univ Med Sci
December 2024
Universitas Nasional, Department of Biology, South Jakarta, Indonesia.
Objectives: Dementia, a growing concern globally, affects more than 55 million people-a number projected to rise to 152 million by 2050. Current medications target Alzheimer's disease, the most prevalent form of dementia. This study investigated L.
View Article and Find Full Text PDFDiscovery of highly potent phosphodiesterase-1 inhibitors by a combined-structure free energy perturbation approach.
Acta Pharm Sin B
December 2024
State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Accurate receptor/ligand binding free energy calculations can greatly accelerate drug discovery by identifying highly potent ligands. By simulating the change from one compound structure to another, the relative binding free energy (RBFE) change can be calculated based on the theoretically rigorous free energy perturbation (FEP) method. However, existing FEP-RBFE approaches may face convergence challenges due to difficulties in simulating non-physical intermediate states, which can lead to increased computational costs to obtain the converged results.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!