On the development of protein pKa calculation algorithms.

scientific article

On the development of protein pKa calculation algorithms. is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1002/PROT.23091
P932PMC publication ID3193850
P698PubMed publication ID21744393

P50authorDamien FarrellQ57419750
Jens Erik NielsenQ73003447
Nathan BakerQ28318462
P2093author name stringYong Huang
Tommy Carstensen
P2860cites workCalculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centersQ52210542
Improving the accuracy of protein pKa calculations: conformational averaging versus the average structureQ52234205
Determination of electrostatic interaction energies and protonation state populations in enzyme active sites.Q54428935
Titration_DB: Storage and analysis of NMR-monitored protein pH titration curvesQ57975710
Rational modification of enzyme catalysis by engineering surface chargeQ58975571
On the calculation of pKas in proteinsQ72074160
Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titrationQ73319277
Electrostatics of nanosystems: application to microtubules and the ribosomeQ24555224
H++: a server for estimating pKas and adding missing hydrogens to macromoleculesQ24813167
PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa valuesQ25257782
Very fast prediction and rationalization of pKa values for protein-ligand complexesQ27144110
The Effect of Structure upon the Reactions of Organic Compounds. Benzene DerivativesQ29013760
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulationsQ29617524
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objectsQ29618574
Toward the accurate first-principles prediction of ionization equilibria in proteins.Q30355994
Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculationsQ30399241
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structuresQ30426168
Incorporating protein conformational flexibility into the calculation of pH-dependent protein propertiesQ30427121
Benchmarking pK(a) prediction.Q30817050
Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studiesQ33665947
Charges in the hydrophobic interior of proteinsQ34136707
Constant pH molecular dynamics with proton tautomerismQ34350350
On the evaluation and optimization of protein X-ray structures for pKa calculationsQ36559778
Electric fields at the active site of an enzyme: direct comparison of experiment with theory.Q39134241
Redesigning protein pKa values.Q42014561
A summary of the measured pK values of the ionizable groups in folded proteinsQ42097166
MCCE2: improving protein pKa calculations with extensive side chain rotamer samplingQ42541149
Constant pH molecular dynamics in generalized Born implicit solventQ43734394
The determinants of pKas in proteinsQ43795561
Benchmarking pKa Prediction Methods for Residues in Proteins.Q45935847
Titration_DB: storage and analysis of NMR-monitored protein pH titration curvesQ46525599
Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solventQ51672152
Acidic range titration of HEWL using a constant-pH molecular dynamics methodQ51896285
The determinants of alpha-amylase pH-activity profilesQ52056321
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.Q52064388
P433issue12
P407language of work or nameEnglishQ1860
P921main subjectalgorithmQ8366
P304page(s)3287-3298
P577publication date2011-07-08
P1433published inProteinsQ7251514
P1476titleOn the development of protein pKa calculation algorithms
P478volume79

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cites work (P2860)
Q34220542A collaborative environment for developing and validating predictive tools for protein biophysical characteristics
Q59042601Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine
Q30352859Bayesian model aggregation for ensemble-based estimates of protein pKa values.
Q26853115Biomolecular electrostatics and solvation: a computational perspective
Q47993096DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
Q44875489Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.
Q48327241Fast coarse-grained model for RNA titration
Q51433975Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.
Q30354510Protein dielectric constants determined from NMR chemical shift perturbations
Q36150734Rapid calculation of protein pKa values using Rosetta
Q37946320The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins

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