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.
The 44 checked references that resolve
resolves10.1021/ar010030mFree Energy Simulations Come of Age: Protein−Ligand Recognition
resolves10.1021/ja981844+Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
resolves10.1021/ja025660dMolecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution
resolves10.1016/j.theochem.2007.12.005Molecular dynamics simulations and MM–PBSA calculations of the cyclodextrin inclusion complexes with 1-alkanols, para-substituted phenols and substituted imidazoles
resolves10.1016/S0006-3495(04)74084-9Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
resolves10.1016/S0022-2836(03)00610-7Insights into Protein–Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras–Raf and Ras–RalGDS Complexes
resolves10.1021/cr960370zMolecular Recognition of Protein−Ligand Complexes: Applications to Drug Design
resolves10.1006/jmbi.2001.4560High affinity T cell receptors from yeast display libraries block T cell activation by superantigens11Edited by I. A. Wilson
resolves10.1016/j.str.2005.08.015Structural Basis of Affinity Maturation and Intramolecular Cooperativity in a Protein-Protein Interaction
resolves10.1074/jbc.M306848200Dissecting Cooperative and Additive Binding Energetics in the Affinity Maturation Pathway of a Protein-Protein Interface
resolves10.1021/ja034729uRole of Water Mediated Interactions in Protein−Protein Recognition Landscapes
resolves10.1006/jmbi.1997.1028Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope
resolves10.1021/jm00017a020The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A
resolves10.1110/ps.04912605Thermodynamic consequences of disrupting a water‐mediated hydrogen bond network in a protein:pheromone complex
resolves10.1021/bi981848rStructure-Based Design of Potent Inhibitors of Scytalone Dehydratase: Displacement of a Water Molecule from the Active Site
resolves10.1021/ja00086a004Structure-Based Design of Synthetic Azobenzene Ligands for Streptavidin
resolves10.1021/ja049701cHydration Free Energies and Entropies for Water in Protein Interiors
resolves10.1063/1.445869Comparison of simple potential functions for simulating liquid water
resolves10.1063/1.470648Constant pressure molecular dynamics simulation: The Langevin piston method
resolves10.1080/08927029108022142Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions
resolves10.1063/1.464397Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems
resolves10.1073/pnas.0600118103Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
resolves10.1021/ja990935jComputational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies
resolves10.1021/jp046377zEvaluation of Poisson Solvation Models Using a Hybrid Explicit/Implicit Solvent Method
resolves10.1002/bip.360350205Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations
resolves10.1002/cphc.200600298Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules
resolves10.1021/jp0717185How Protein Surfaces Induce Anomalous Dynamics of Hydration Water
resolves10.1021/jp055399yDynamics of Water Confined in the Interdomain Region of a Multidomain Protein
resolves10.1063/1.2198802Simulation studies of the protein-water interface. I. Properties at the molecular resolution
resolves10.1063/1.1587119Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
resolves10.1002/jcc.10379Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf
resolves10.1021/ja0377908Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method
The 2 references without a DOI — listed, not checked
no DOI — not checkedCase, D. A.; Darden, T.; Cheatham, T. E., III.; Simmerling, C.; Wang, J.; Duke, R.; Luo, R.; Merz, K.; Pearlman, D.; Crowley, M.; Walker, R.; Zhang, W.; Wang, B.; Hayik, A.; Roiberg, A.; Seabra, G.; Wong, K.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Morgan, J.; Hornak, V.; Cui, G.; Beroza, P.; Matthews, D.; Schfmeister, C.; Ross, W.; Kollman, P.AMBER 9; 2006.
no DOI — not checkedKonecny, R.iAPBS interface on the Web. http://mccammon.ucsd.edu/iapbs (accessed April 4, 2008).
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