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High-Throughput Calculation of Protein−Ligand Binding Affinities:  Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing

https://doi.org/10.1021/ci050488t
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18/18 checkable references clean · checked 2026-07-22

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

8 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.

The 18 checked references that resolve
resolves10.1515/9780691227658
Scientific Parallel Computing
resolves10.1016/0010-4825(90)90046-R
A CPU benchmark for protein crystallographic refinement
resolves10.1016/S0010-4655(98)00089-7
Parallel molecular dynamics simulation: Implementation of PVM for a lipid membrane
resolves10.1126/science.282.5389.740
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
resolves10.1002/(SICI)1096-987X(199602)17:3<326::AID-JCC7>3.0.CO;2-X
A new parallel method for molecular dynamics simulation of macromolecular systems
resolves10.1002/bip.10219
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
resolves10.1021/jm030827e
Discovery of a Potent and Selective Protein Kinase CK2 Inhibitor by High-Throughput Docking
resolves10.1021/ja981844+
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
resolves10.1021/ar000033j
Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models
resolves10.1002/0470867167.ch11
Condor and the Grid
resolves10.1021/jm000241h
Binding of a Diverse Set of Ligands to Avidin and Streptavidin:  An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
resolves10.1021/jm049081q
Validation and Use of the MM-PBSA Approach for Drug Discovery
resolves10.1073/pnas.71.8.2925
Empirical Correlation Between Hydrophobic Free Energy and Aqueous Cavity Surface Area
resolves10.1016/0301-4622(94)00062-X
Correlating solvation free energies and surface tensions of hydrocarbon solutes
resolves10.1016/0010-4655(95)00041-D
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
resolves10.1002/jcc.10349
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
resolves10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
resolves10.1002/jcc.20035
Development and testing of a general amber force field
The 8 references without a DOI — listed, not checked
no DOI — not checkedComputer Simulation of Liquids
no DOI — not checkedci050488tb00005/ci050488tb00005_1
no DOI — not checkedci050488tb00008/ci050488tb00008_1
no DOI — not checkedhttp:// www.eyesopen.com/ (accessed
no DOI — not checkedFunct., Bioinf.
no DOI — not checkedhttp://www.intel.com/cd/software/products/asmo-na/eng/compilers/flin/index.htm (accessed
no DOI — not checkedhttp://cygwin.com/ (accessed
no DOI — not checkedhttp://www.absoft.com/Products/Compilers/Fortran/Windows/windows.html (accessed
What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

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