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Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect

https://doi.org/10.1002/prot.24848
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.20026openalex-snapshot
Efficient approximate all‐atom solvent accessible surface area method parameterized for folded and denatured protein conformations
inferredcites →https://doi.org/10.1002/jcc.23108openalex-snapshot
FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm
inferredcites →https://doi.org/10.1002/jcc.540100804openalex-snapshot
Validation of the general purpose tripos 5.2 force field
inferredcites →https://doi.org/10.1002/pro.257openalex-snapshot
Quantitative prediction of protein–protein binding affinity with a potential of mean force considering volume correction
inferredcites →https://doi.org/10.1002/prot.10031openalex-snapshot
Potential of mean force for protein–protein interaction studies
inferredcites →https://doi.org/10.1007/s00894-004-0214-9openalex-snapshot
An extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model
inferredcites →https://doi.org/10.1007/s00894-014-2251-3openalex-snapshot
A comparison of various optimization algorithms of protein–ligand docking programs by fitness accuracy
inferredcites →https://doi.org/10.1007/s00894-014-2361-yopenalex-snapshot
Insight into the informational-structure behavior of the Diels-Alder reaction of cyclopentadiene and maleic anhydride
inferredcites →https://doi.org/10.1016/0022-2836(71)90324-xopenalex-snapshot
The interpretation of protein structures: Estimation of static accessibility
inferredcites →https://doi.org/10.1016/0300-9084(96)88166-1openalex-snapshot
Principles of protein-protein recognition from structure to thermodynamics
inferredcites →https://doi.org/10.1016/j.sbi.2004.03.009openalex-snapshot
Recent advances in the development and application of implicit solvent models in biomolecule simulations
inferredcites →https://doi.org/10.1016/j.sbi.2014.05.009openalex-snapshot
Design and designability of protein-based assemblies
inferredcites →https://doi.org/10.1016/s0006-3495(97)78756-3openalex-snapshot
The statistical-thermodynamic basis for computation of binding affinities: a critical review
inferredcites →https://doi.org/10.1016/s0022-2836(05)80269-4openalex-snapshot
Calculation of conformational ensembles from potentials of mena force
inferredcites →https://doi.org/10.1021/ar000033jopenalex-snapshot
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
inferredcites →https://doi.org/10.1021/ci100264eopenalex-snapshot
Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets
inferredcites →https://doi.org/10.1021/ci100354xopenalex-snapshot
Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models
inferredcites →https://doi.org/10.1021/ci200057eopenalex-snapshot
Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions
inferredcites →https://doi.org/10.1021/ci200082topenalex-snapshot
CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
inferredcites →https://doi.org/10.1021/ci400120bopenalex-snapshot
SFCscore RF : A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes
inferredcites →https://doi.org/10.1021/ci500080qopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
inferredcites →https://doi.org/10.1021/ci500081mopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
inferredcites →https://doi.org/10.1021/ci500091ropenalex-snapshot
Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
inferredcites →https://doi.org/10.1021/ci500406kopenalex-snapshot
Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes
inferredcites →https://doi.org/10.1021/ci500731aopenalex-snapshot
Classification of Current Scoring Functions
inferredcites →https://doi.org/10.1021/ja034729uopenalex-snapshot
Role of Water Mediated Interactions in Protein−Protein Recognition Landscapes
inferredcites →https://doi.org/10.1021/ja075302gopenalex-snapshot
Metal-Coupled Folding of Cys 2 His 2 Zinc-Finger
inferredcites →https://doi.org/10.1021/ja984102popenalex-snapshot
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot
The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot
A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
inferredcites →https://doi.org/10.1021/jp0102318openalex-snapshot
Solvation Model Based on Weighted Solvent Accessible Surface Area
inferredcites →https://doi.org/10.1021/jp025595uopenalex-snapshot
Empirical Aqueous Solvation Models Based on Accessible Surface Areas with Implicit Electrostatics
inferredcites →https://doi.org/10.1038/14918openalex-snapshot
A computational approach to simplifying the protein folding alphabet.
inferredcites →https://doi.org/10.1038/319199a0openalex-snapshot
Solvation energy in protein folding and binding
inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot
Virtual screening of chemical libraries
inferredcites →https://doi.org/10.1038/nature04818openalex-snapshot
Computational redesign of endonuclease DNA binding and cleavage specificity
inferredcites →https://doi.org/10.1038/nature07885openalex-snapshot
Design of protein-interaction specificity gives selective bZIP-binding peptides
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1038/nsb877openalex-snapshot
Automated design of specificity in molecular recognition
inferredcites →https://doi.org/10.1038/nsmb749openalex-snapshot
Computational redesign of protein-protein interaction specificity
inferredcites →https://doi.org/10.1038/srep00309openalex-snapshot
Specificity quantification of biomolecular recognition and its implication for drug discovery
inferredcites →https://doi.org/10.1039/c3sc50478fopenalex-snapshot
Thermodynamic and kinetic specificities of ligand binding
inferredcites →https://doi.org/10.1073/pnas.0506124102openalex-snapshot
Specificity versus stability in computational protein design
inferredcites →https://doi.org/10.1073/pnas.1212842109openalex-snapshot
Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding
inferredcites →https://doi.org/10.1073/pnas.1220699110openalex-snapshot
Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition
inferredcites →https://doi.org/10.1073/pnas.2234277100openalex-snapshot
Exploring the origins of binding specificity through the computational redesign of calmodulin
inferredcites →https://doi.org/10.1093/bioinformatics/btq112openalex-snapshot
A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
inferredcites →https://doi.org/10.1093/bioinformatics/btt121openalex-snapshot
Specificity and affinity quantification of protein–protein interactions
inferredcites →https://doi.org/10.1093/bioinformatics/btu626openalex-snapshot
PDB-wide collection of binding data: current status of the PDBbind database
inferredcites →https://doi.org/10.1093/nar/gki204openalex-snapshot
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
inferredcites →https://doi.org/10.1093/nar/gkj039openalex-snapshot
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB
inferredcites →https://doi.org/10.1093/nar/gku077openalex-snapshot
A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method
inferredcites →https://doi.org/10.1103/physrevlett.90.188101openalex-snapshot
Energy Landscape Theory, Funnels, Specificity, and Optimal Criterion of Biomolecular Binding
inferredcites →https://doi.org/10.1103/physrevlett.99.198101openalex-snapshot
Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening
inferredcites →https://doi.org/10.1146/annurev.biophys.34.040204.144517openalex-snapshot
MODELING WATER, THE HYDROPHOBIC EFFECT, AND ION SOLVATION
inferredcites →https://doi.org/10.1146/annurev.biophys.35.040405.102134openalex-snapshot
WATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION
inferredcites →https://doi.org/10.1146/annurev.physchem.49.1.531openalex-snapshot
COMPUTER SIMULATIONS WITH EXPLICIT SOLVENT: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects
inferredcites →https://doi.org/10.1146/annurev.physchem.58.032806.104445openalex-snapshot
Dewetting and Hydrophobic Interaction in Physical and Biological Systems
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1371/journal.pone.0074443openalex-snapshot
Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity
inferredcites →https://doi.org/10.1517/17460441.2010.484460openalex-snapshot
Virtual screening with AutoDock: theory and practice
inferredcites →https://doi.org/10.1517/17460441.2013.794780openalex-snapshot
Automated docking for novel drug discovery
inferredcites →https://doi.org/10.2174/13816128113199990599openalex-snapshot
Solvation Models: Theory and Validation

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.24667openalex-snapshot
Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest
inferred← citeshttps://doi.org/10.1002/wcms.1225openalex-snapshot
Machine‐learning scoring functions to improve structure‐based binding affinity prediction and virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-016-9897-0openalex-snapshot
Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
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Forging the Basis for Developing Protein–Ligand Interaction Scoring Functions
inferred← citeshttps://doi.org/10.1038/s41598-021-82410-1openalex-snapshot
New machine learning and physics-based scoring functions for drug discovery
inferred← citeshttps://doi.org/10.1039/c7cp08170gopenalex-snapshot
Toward a unified scoring function for native state discrimination and drug-binding pocket recognition
inferred← citeshttps://doi.org/10.1088/1361-6633/ac3800openalex-snapshot
Physics of biomolecular recognition and conformational dynamics
inferred← citeshttps://doi.org/10.1093/nar/gkx255openalex-snapshot
SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity
inferred← citeshttps://doi.org/10.3390/ijms21249548openalex-snapshot
DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch009openalex-snapshot
Scoring Functions of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch036openalex-snapshot
Scoring Functions of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.52711/2231-5659.2025.00041openalex-snapshot
Review on the Evolving Landscape of Molecular Docking in Drug Discovery
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.