The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-61779-465-0_27 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Regioselective Suzuki-Miyarua Cross-Coupling for Substituted 2,4-Dibromopyridines Catalyzed by -Symmetric Tripalladium Clusters.
J Org Chem
January 2025
Department of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, Liaocheng University, Liaocheng 252059, China.
Multipalladium clusters possess peculiar structures and synergistic effects for reactivity and selectivity. Herein, -symmetric tripalladium clusters (, 0.5 mol %) afford C-regioselective SMCC of 2,4-dibromopyridine with phenylboronic acids or pinacol esters (C:C up to 98:1), in contrast to Pd(OAc) in ligand-free conditions.
View Article and Find Full Text PDFHeterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element.
Proc Natl Acad Sci U S A
January 2025
Department of Chemistry, New York University, New York, NY 10003.
Frameshifting is an essential mechanism employed by many viruses including coronaviruses to produce viral proteins from a compact RNA genome. It is facilitated by specific RNA folds in the frameshift element (FSE), which has emerged as an important therapeutic target. For SARS-CoV-2, a specific 3-stem pseudoknot has been identified to stimulate frameshifting.
View Article and Find Full Text PDF"Jiedutongluo Tiaoying Formula" (JDTLTYF) TCM prescriptions can effectively treat hyperthyroidism and effectively improve the condition of patients. The main active ingredients of JDTLTYF were collected from the TCMSP database and the target was predicted. Genes related to hyperthyroidism were identified using DisGeNET, GeneCards and OMIM databases.
View Article and Find Full Text PDFRevealing the Surface Reconstruction on the High OER Catalytic Activity of Ni3S2.
ChemSusChem
January 2025
Sun Yat-Sen University, School of Materials Science and Engineering, No. 135, Xingang Xi Road, China, 510006, Guangzhou, CHINA.
Sluggish oxygen evolution reaction (OER) is a crucial part of water splitting and solar fuel generation, which limits their utilization. Ni3S2 is a promising OER catalyst, in which surface reconstruction is an important step to improve performance. In this study, DFT calculations were employed to investigate the effect of surface reconstruction on (001), (110), and (101) surfaces of Ni3S2 in alkaline OER.
View Article and Find Full Text PDFInterface Engineering and Modulation of Nickel Oxide for High Air-Stable p-Type Crystalline Silicon Solar Cells.
Small
January 2025
Anhui Soltrend New Energy Technology Co., Ltd, Lujiang County, Hefei, 230000, China.
Dopant-free passivating contact crystalline silicon solar cells hold the potential of higher efficiency and cost down. In the hole-transport terminal, one still faces the challenge of trade-off between efficiency and stability. In this work, a H-AlO/NiO/Ni stacked hole-transport layer is proposed, where the H-AlO standing for H-rich AlO film can effectively reduce the interfacial defects and the high work function Ni metal results in a low contact resistance of 47.
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!