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Ligand–Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging

https://doi.org/10.1021/ci500301s
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-hopenalex-snapshot
LINCS: A linear constraint solver for molecular simulations
inferredcites →https://doi.org/10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-fopenalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.20047openalex-snapshot
Binding affinity prediction with different force fields: Examination of the linear interaction energy method
inferredcites →https://doi.org/10.1002/jcc.20634openalex-snapshot
A semiempirical free energy force field with charge‐based desolvation
inferredcites →https://doi.org/10.1002/jcc.20893openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/jcc.21367openalex-snapshot
CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields
inferredcites →https://doi.org/10.1002/jcc.21450openalex-snapshot
Basic ingredients of free energy calculations: A review
inferredcites →https://doi.org/10.1002/jcc.21643openalex-snapshot
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
inferredcites →https://doi.org/10.1002/prot.20033openalex-snapshot
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
inferredcites →https://doi.org/10.1002/prot.20688openalex-snapshot
Molecular docking of balanol to dynamics snapshots of protein kinase A
inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot
Protein–ligand docking: Current status and future challenges
inferredcites →https://doi.org/10.1002/prot.22826openalex-snapshot
Flexibility and inhibitor binding in cdc25 phosphatases
inferredcites →https://doi.org/10.1002/prot.340230315openalex-snapshot
The use of position‐specific rotamers in model building by homology
inferredcites →https://doi.org/10.1006/jmbi.1998.2172openalex-snapshot
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0378-4754(93)90043-topenalex-snapshot
Numerical recipes in Fortran (The art of scientific computing)
inferredcites →https://doi.org/10.1016/j.cell.2012.03.016openalex-snapshot
Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution
inferredcites →https://doi.org/10.1016/j.drudis.2009.01.003openalex-snapshot
Managing protein flexibility in docking and its applications
inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
inferredcites →https://doi.org/10.1016/j.jmb.2006.05.023openalex-snapshot
The Geometry of the Ribosomal Polypeptide Exit Tunnel
inferredcites →https://doi.org/10.1016/j.jmb.2007.06.002openalex-snapshot
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
inferredcites →https://doi.org/10.1016/j.jmb.2009.09.049openalex-snapshot
Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferredcites →https://doi.org/10.1016/j.sbi.2008.11.009openalex-snapshot
Computational evaluation of protein–small molecule binding
inferredcites →https://doi.org/10.1016/j.sbi.2011.01.010openalex-snapshot
Advances in all atom sampling methods for modeling protein–ligand binding affinities
inferredcites →https://doi.org/10.1016/j.sbi.2011.01.011openalex-snapshot
Alchemical free energy methods for drug discovery: progress and challenges
inferredcites →https://doi.org/10.1016/s0006-3495(03)75033-4openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0022-2836(02)00777-5openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0022-2836(02)01408-0openalex-snapshot
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inferredcites →https://doi.org/10.1021/ar010014popenalex-snapshot
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inferredcites →https://doi.org/10.1021/bi001351topenalex-snapshot
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inferredcites →https://doi.org/10.1021/ci500091ropenalex-snapshot
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inferredcites →https://doi.org/10.1021/ct100245nopenalex-snapshot
Modeling Protein−Ligand Binding by Mining Minima
inferredcites →https://doi.org/10.1021/ct100246yopenalex-snapshot
Ensemble Docking from Homology Models
inferredcites →https://doi.org/10.1021/ct1002913openalex-snapshot
Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities
inferredcites →https://doi.org/10.1021/ct300024zopenalex-snapshot
The Effects of Computational Modeling Errors on the Estimation of Statistical Mechanical Variables
inferredcites →https://doi.org/10.1021/ct300783eopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ct600258eopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm000942eopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm0491187openalex-snapshot
Decoys for Docking
inferredcites →https://doi.org/10.1021/jm049726mopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm070654jopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm800562dopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp0006274openalex-snapshot
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inferredcites →https://doi.org/10.1021/jp011480zopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp056929topenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp807701hopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp901322vopenalex-snapshot
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inferredcites →https://doi.org/10.1038/355371a0openalex-snapshot
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inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
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inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot
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inferredcites →https://doi.org/10.1039/b511805kopenalex-snapshot
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inferredcites →https://doi.org/10.1063/1.2221680openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.2221683openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.2408420openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.328693openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.459255openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1063/1.4751284openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.479199openalex-snapshot
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inferredcites →https://doi.org/10.1073/pnas.0609752104openalex-snapshot
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inferredcites →https://doi.org/10.1073/pnas.71.8.2925openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/btt055openalex-snapshot
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.1096361openalex-snapshot
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inferredcites →https://doi.org/10.1146/annurev-biophys-042910-155255openalex-snapshot
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inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
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inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pcbi.1000634openalex-snapshot
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inferredcites →https://doi.org/10.2174/1386207053328183openalex-snapshot
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inferredcites →https://doi.org/10.2174/138945008786949360openalex-snapshot
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inferredcites →https://doi.org/10.2307/2265725openalex-snapshot
Biostatistical Analysis
inferredcites →https://doi.org/10.2307/2289268openalex-snapshot
Biostatistical Analysis (2nd ed.).

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/jcc.25139openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26779openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26957openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ptr.6220openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-1209-5_10openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bpj.2018.01.014openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.cjph.2021.07.027openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00562openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00639openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00292openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00655openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00314openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00764openalex-snapshot
From Brazil to Germany: Challenges and Advantages
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c02009openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41598-023-33333-6openalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c5nr02970hopenalex-snapshot
Shape effect in cellular uptake of PEGylated nanoparticles: comparison between sphere, rod, cube and disk
inferred← citeshttps://doi.org/10.11606/t.46.2016.tde-03082016-145527openalex-snapshot
Bioquímica e biofísica computacionais: simulações da reatividade e da estrutura de biomoléculas
inferred← citeshttps://doi.org/10.11606/t.46.2016.tde-22082016-080806openalex-snapshot
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inferred← citeshttps://doi.org/10.11606/t.46.2018.tde-14122017-135400openalex-snapshot
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inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-bhb1jopenalex-snapshot
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inferred← citeshttps://doi.org/10.26434/chemrxiv.14208446openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fmolb.2020.00114openalex-snapshot
Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.3389/fphar.2018.01089openalex-snapshot
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