| Item Type | Name |
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Concept
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Membrane Proteins
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Concept
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DNA-Binding Proteins
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Concept
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Mitochondrial Proteins
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Concept
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Carrier Proteins
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Concept
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Nuclear Proteins
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Concept
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Mutant Proteins
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Concept
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Intracellular Signaling Peptides and Proteins
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Concept
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Plasma Membrane Neurotransmitter Transport Proteins
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Concept
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Egg Proteins
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Concept
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Proteins
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Concept
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Zebrafish Proteins
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Concept
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Membrane Transport Proteins
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Concept
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Bacterial Proteins
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Concept
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Photosynthetic Reaction Center Complex Proteins
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Concept
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Microfilament Proteins
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Concept
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Nerve Tissue Proteins
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Concept
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Tumor Suppressor Proteins
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Concept
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RNA-Binding Proteins
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Academic Article
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Predicting folding free energy changes upon single point mutations.
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Academic Article
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Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.
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Academic Article
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A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins.
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Academic Article
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Modeling the effects of mutations on the free energy of the first electron transfer from QA- to QB in photosynthetic reaction centers.
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Academic Article
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Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers.
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Academic Article
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Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides.
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Academic Article
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Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s.
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Academic Article
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Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling.
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Academic Article
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On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles.
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Academic Article
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Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure.
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Academic Article
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Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes.
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Academic Article
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Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain.
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Academic Article
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Electrostatic properties of protein-protein complexes.
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Academic Article
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Comparative study of generalized born models: Born radii and peptide folding.
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Academic Article
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Predicting 3D structures of transient protein-protein complexes by homology.
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Academic Article
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Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives.
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Academic Article
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Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.
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Academic Article
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Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families.
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Academic Article
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Optimization of electrostatic interactions in protein-protein complexes.
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Academic Article
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Protein-protein interactions.
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Academic Article
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Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions.
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Academic Article
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Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.
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Academic Article
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On the pH-optimum of activity and stability of proteins.
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Academic Article
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In silico modeling of pH-optimum of protein-protein binding.
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Academic Article
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A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics.
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Academic Article
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Developing hybrid approaches to predict pKa values of ionizable groups.
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Academic Article
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Progress in the prediction of pKa values in proteins.
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Academic Article
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Analyzing effects of naturally occurring missense mutations.
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Academic Article
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Predicting nonspecific ion binding using DelPhi.
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Academic Article
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Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.
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Academic Article
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BION web server: predicting non-specifically bound surface ions.
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Academic Article
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A rational free energy-based approach to understanding and targeting disease-causing missense mutations.
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Academic Article
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Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi.
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Academic Article
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Cancer missense mutations alter binding properties of proteins and their interaction networks.
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Academic Article
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Molecular mechanisms of disease-causing missense mutations.
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Academic Article
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Protonation and pK changes in protein-ligand binding.
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Academic Article
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Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity.
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Academic Article
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ProBLM web server: protein and membrane placement and orientation package.
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Academic Article
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Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins.
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Academic Article
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ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons.
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Academic Article
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Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.
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Academic Article
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pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.
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Academic Article
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Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence.
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Academic Article
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DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.
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Academic Article
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Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding.
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Academic Article
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SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.
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Academic Article
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SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.
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Academic Article
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On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi.
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Academic Article
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On the electrostatic properties of homodimeric proteins.
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Academic Article
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Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.
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Academic Article
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Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model.
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Academic Article
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DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.
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Academic Article
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A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential.
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Academic Article
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DelPhiForce web server: electrostatic forces and energy calculations and visualization.
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Academic Article
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Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.
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Academic Article
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DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate.
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Academic Article
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Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases.
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Academic Article
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PKAD: a database of experimentally measured pKa values of ionizable groups in proteins.
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Academic Article
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A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.
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Academic Article
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SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability.
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Academic Article
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Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.
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Academic Article
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BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics.
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Academic Article
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On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary.
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Academic Article
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Increased p53 signaling impairs neural differentiation in HUWE1-promoted intellectual disabilities.
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Academic Article
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SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions.
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Academic Article
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Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi.
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Academic Article
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SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity.
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Academic Article
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Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease.
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Academic Article
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Electrostatics in Computational Biophysics and Its Implications for Disease Effects.
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