Reference health
Calculation of absolute protein–ligand binding free energy from computer simulations
2 of 45 checkable references need attention · checked 2026-07-22
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
1 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
does not resolve to a known work10.1021/ja963568
does not resolve to a known work10.1021/jm040008
The 43 checked references that resolve
resolves10.1146/annurev.med.53.052901.131947
Rational Approach to AIDS Drug Design Through Structural Biology
resolves10.1126/science.1083653
Assembly of Cell Regulatory Systems Through Protein Interaction Domains
resolves10.1023/A:1008763014207
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
resolves10.1021/cr00023a004
Free energy calculations: Applications to chemical and biochemical phenomena
resolves10.1002/ijch.198600032
The Free Energy of Xenon Binding to Myoglobin from Molecular Dynamics Simulation
resolves10.1021/ja9738539
Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy
resolves10.1016/S0006-3495(96)79267-6
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study
resolves10.1021/jp0217839
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
resolves10.1006/jmbi.2000.4064
Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 Lysozyme L99A
resolves10.1006/jmbi.1999.3190
Investigation of phosphotyrosine recognition by the SH2 domain of the Src kinase 1 1Edited by P. E. Wright
resolves10.1016/0092-8674(93)90405-F
Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: Crystal structures of the complexed and peptide-free forms
resolves10.1006/jmbi.1996.0112
Crystal Structures of the Human p56lckSH2 Domain in Complex with Two Short Phosphotyrosyl Peptides at 1.0 Å and 1.8 Å Resolution
resolves10.1016/j.jmb.2003.09.075
Sequence, Structure and Energetic Determinants of Phosphopeptide Selectivity of SH2 Domains
resolves10.1021/bi9620868
Determination of Affinities for <i>lck </i>SH2 Binding Peptides Using a Sensitive Fluorescence Assay: Comparison between the pYEEIP and pYQPQP Consensus Sequences Reveals Context-Dependent Binding Specificity
resolves10.1021/bi9814991
Calorimetric Investigation of Proton Linkage by Monitoring both the Enthalpy and Association Constant of Binding: Application to the Interaction of the Src SH2 Domain with a High-Affinity Tyrosyl Phosphopeptide
resolves10.1016/S0006-3495(04)74084-9
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
resolves10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y
Reduced surface: An efficient way to compute molecular surfaces
resolves10.1002/jcc.540040211
<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations
resolves10.1021/jp973084f
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
resolves10.1021/jp9711499
Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding.
resolves10.1016/0021-9991(77)90121-8
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
resolves10.1002/jcc.540130812
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
resolves10.1016/0010-4655(95)00053-I
The calculation of the potential of mean force using computer simulations
resolves10.1063/1.466711
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
resolves10.1021/jp970736r
Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations
resolves10.1063/1.454895
Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
resolves10.1021/ja00192a057
Interactions between amides in solution and the thermodynamics of weak binding
resolves10.1016/S0006-3495(97)78756-3
The statistical-thermodynamic basis for computation of binding affinities: a critical review
The 1 reference without a DOI — listed, not checked
no DOI — not checkedCarlson, H. A. & McCammon, J. A. (2000) Mol. Pharmacol. 57, 213–218.10648630
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