• Corpus ID: 112124465

Explorator yStudie so fA bIniti oProtei nStructure Prediction :Multipl eCop ySimulate dAnnealing ,AMBER Energ yFunctions ,an da Generalize dBorn/Solvent Accessibilit ySolvatio nModel

  title={Explorator yStudie so fA bIniti oProtei nStructure Prediction :Multipl eCop ySimulate dAnnealing ,AMBER Energ yFunctions ,an da Generalize dBorn/Solvent Accessibilit ySolvatio nModel},
  author={L. Beveridge},
Atheoretica lan dcomputational approac ht oa biniti ostructur epredictio nfor polypeptide si nwate ri sdescribe dan dapplie dto selecte damin oaci dsequence sfo rtestin gan dpre- liminar yvalidation .Th emetho dbuild ssystemati- call yo nth eextensiv eeffort sapplie dt oparameter- izatio no fmolecula rdynamic s(MD )forc efields, employ sa nempiricall ywell-validate dcontinuum dielectri cmode lfo rsolvation ,an da neminently parallelizabl eapproac ht oconformationa lsearch. Th eeffectiv efre… 


Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields
The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1
A combined method for the prediction of protein tertiary structures from sequence is presented. This multistep procedure initially uses a simplified approach to protein structure prediction,
Comparing search strategies for finding global optima on energy landscapes
We provide some tests of the convex global underestimator (CGU) algorithm, which aims to find global minima on funnel‐shaped energy landscapes. We use two different potential functions—the reduced
RMS/Coverage graphs: A qualitative method for comparing three‐dimensional protein structure predictions
A method is described that captures the best results from a large number of alternative sequence‐dependent structural superpositions between a prediction and the experimental structure and represents them as a single line on a graph.
Use of MM‐PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
This work investigates the stability of three different ensembles of the 36‐mer villin headpiece subdomain, the native, a compact folding intermediate, and the random coil, finding the native ensemble to be ≈26 kcal/mol more stable than the folding intermediate and ≈39 kcal/ mol morestable than the random Coil ensemble.
Statistical potentials extracted from protein structures: how accurate are they?
It is found that complex residue-residue distance dependences observed in statistical potentials can be largely explained as an indirect consequence of the burial of non-polar groups.
Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
It is shown that for large enough databases the contact approximation to the energy cannot stabilize all the native folds even against the decoys obtained by gapless threading.
Processing and analysis of CASP3 protein structure predictions
The essentials of the approach are outlined, with discussion of the superposition procedures, definitions of basic measures, and descriptions of new methods developed to analyze predictions, on the evaluation of threedimensional models and secondary structure predictions.
Ab initio protein structure prediction of CASP III targets using ROSETTA
Results suggest that ab initio methods may soon become useful for low‐resolution structure prediction for proteins that lack a close homologue of known structure.
From Levinthal to pathways to funnels
The general energy landscape picture provides a conceptual framework for understanding both two-state and multi-state folding kinetics and hopes to learn much more about the real shapes of protein folding landscapes.