A statistical mechanical method to optimize energy functions for protein folding

scientific article published on April 2000

A statistical mechanical method to optimize energy functions for protein folding is …
instance of (P31):
scholarly articleQ13442814

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P819ADS bibcode2000PNAS...97.3977B
P356DOI10.1073/PNAS.97.8.3977
P932PMC publication ID18127
P698PubMed publication ID10760269
P5875ResearchGate publication ID12556689

P2093author name stringVendruscolo M
Knapp EW
Bastolla U
P2860cites workProtein Folding in Contact Map SpaceQ21698714
Errors in protein structuresQ27860776
Principles that govern the folding of protein chainsQ28236872
A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional StructureQ28282741
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solutionQ28286232
From Levinthal to pathways to funnelsQ28300934
How to derive a protein folding potential? A new approach to an old problemQ30426274
Recovery of protein structure from contact mapsQ30428899
Self-consistently optimized energy functions for protein structure prediction by molecular dynamicsQ30429818
Designing potential energy functions for protein foldingQ33632621
Spin glasses and the statistical mechanics of protein foldingQ34358450
On the thermodynamic hypothesis of protein foldingQ36091068
Enlarged representative set of protein structuresQ36278475
Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemesQ36281424
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?Q36850366
Optimal protein-folding codes from spin-glass theoryQ37035526
Protein tertiary structure recognition using optimized Hamiltonians with local interactionsQ37219203
An iterative method for extracting energy-like quantities from protein structures.Q37262313
How optimization of potential functions affects protein foldingQ37611237
On the theory of folding kinetics for short proteins.Q46019059
Testing a new Monte Carlo algorithm for protein foldingQ47810344
Simulations of the folding of a globular proteinQ47890039
Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?Q52082394
Protein folding mechanisms and the multidimensional folding funnel.Q52237311
Contact potential that recognizes the correct folding of globular proteinsQ52412013
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.Q52451138
"New view" of protein folding reconciled with the old through multiple unfolding simulations.Q52528318
Master Equation Approach to Protein Folding and Kinetic TrapsQ58495842
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean forceQ68363646
Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice modelQ73174194
Factors that affect the folding ability of proteinsQ74631425
Protein dynamics with off-lattice Monte Carlo movesQ78077224
P433issue8
P407language of work or nameEnglishQ1860
P921main subjectstatisticsQ12483
protein foldingQ847556
P304page(s)3977-3981
P577publication date2000-04-01
P1433published inProceedings of the National Academy of Sciences of the United States of AmericaQ1146531
P1476titleA statistical mechanical method to optimize energy functions for protein folding
P478volume97

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cites work (P2860)
Q47304975A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.
Q42708071Assessment of the quality of energy functions for protein folding by using a criterion derived with the help of the noisy go model
Q28241164Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints
Q38223691Detecting selection on protein stability through statistical mechanical models of folding and evolution
Q30420867Distance dependency and minimum amino acid alphabets for decoy scoring potentials
Q57953582Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
Q31922968How to guarantee optimal stability for most representative structures in the Protein Data Bank.
Q57483275Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution
Q57218694Lack of self-averaging in neutral evolution of proteins
Q33692707Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.
Q35222696On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding
Q30371877Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.
Q30400418Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions
Q52076418Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies.
Q22066374Reductive genome evolution in Buchnera aphidicola
Q47720602Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding
Q30404525Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures
Q29615145Statistical potential for assessment and prediction of protein structures
Q35635713Statistical potential for modeling and ranking of protein-ligand interactions
Q30385705Statistical potentials for improved structurally constrained evolutionary models.
Q47982690Statistical properties of neutral evolution
Q47222730Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data
Q21686181Teaching computers to fold proteins
Q37037782Why should we care about molecular coevolution?
Q42023667toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map.

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