ArticleJournal of chemical information and modeling2013
Improving protocols for protein mapping through proper comparison to crystallography data.
Article in Journal of chemical information and modeling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms.The journal of physical chemistry. B · 2024Article
- FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures.Journal of molecular biology · 2022Article
- Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.New journal of chemistry = Nouveau journal de chimie · 2022Article
- Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2021Article
- Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.Journal of chemical information and modeling · 2020Article
- Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization.Journal of chemical information and modeling · 2019Article
- Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations.Journal of chemical information and modeling · 2019Article
- Deriving Ligand Orientation in Weak Protein-Ligand Complexes by DEEP-STD NMR Spectroscopy in the Absence of Protein Chemical-Shift Assignment.Chembiochem : a European journal of chemical biology · 2019Article
- Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.Journal of chemical information and modeling · 2018Article
- Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification.Journal of chemical theory and computation · 2017Article
- Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics.Journal of medicinal chemistry · 2016Review
- Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.The journal of physical chemistry letters · 2016Article
- Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems.The journal of physical chemistry. B · 2016Article
- Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case.Biopolymers · 2016Article
- Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.Trends in pharmacological sciences · 2015Review
- Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions.Chemistry & biology · 2015Review
- The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.Nature protocols · 2015Article
- Parameter choice matters: validating probe parameters for use in mixed-solvent simulations.Journal of chemical information and modeling · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective-or even erroneous-atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. On the basis of comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future multiple solvent crystallographic structures.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.