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How Fast-Folding Proteins Fold
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1521-3773(19990115)38:1/2<236::aid-anie236>3.0.co;2-mopenalex-snapshot
Peptide Folding: When Simulation Meets Experiment
inferredcites →https://doi.org/10.1002/prot.340230412openalex-snapshot
Knowledge‐based protein secondary structure assignment
inferredcites →https://doi.org/10.1006/jmbi.1998.1645openalex-snapshot
Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright
inferredcites →https://doi.org/10.1006/jmbi.2000.4345openalex-snapshot
The ββα fold: explorations in sequence space11Edited by M. F. Summers
inferredcites →https://doi.org/10.1016/j.bpj.2011.03.051openalex-snapshot
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
inferredcites →https://doi.org/10.1016/j.cplett.2009.02.054openalex-snapshot
Analysis of single molecule folding studies with replica correlation functions
inferredcites →https://doi.org/10.1016/j.febslet.2007.09.027openalex-snapshot
Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis
inferredcites →https://doi.org/10.1016/j.jmb.2005.06.081openalex-snapshot
Transition State Contact Orders Correlate with Protein Folding Rates
inferredcites →https://doi.org/10.1016/j.jmb.2006.03.034openalex-snapshot
Sub-microsecond Protein Folding
inferredcites →https://doi.org/10.1016/j.jmb.2006.06.041openalex-snapshot
Small Proteins Fold Through Transition States With Native-like Topologies
inferredcites →https://doi.org/10.1016/j.jmb.2007.06.032openalex-snapshot
Full-sequence Computational Design and Solution Structure of a Thermostable Protein Variant
inferredcites →https://doi.org/10.1016/j.jmb.2009.02.014openalex-snapshot
Downhill versus Barrier-Limited Folding of BBL
inferredcites →https://doi.org/10.1016/j.jmb.2009.05.011openalex-snapshot
The Folding Mechanism of BBL: Plasticity of Transition-State Structure Observed within an Ultrafast Folding Protein Family
inferredcites →https://doi.org/10.1016/j.jmb.2009.06.058openalex-snapshot
The Limited Role of Nonnative Contacts in the Folding Pathways of a Lattice Protein
inferredcites →https://doi.org/10.1016/j.jmb.2010.10.023openalex-snapshot
Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein
inferredcites →https://doi.org/10.1016/j.sbi.2004.01.002openalex-snapshot
Exploring folding free energy landscapes using computational protein design
inferredcites →https://doi.org/10.1016/j.sbi.2004.01.013openalex-snapshot
The protein folding ‘speed limit’
inferredcites →https://doi.org/10.1016/j.sbi.2010.11.002openalex-snapshot
The folding of single domain proteins—have we reached a consensus?
inferredcites →https://doi.org/10.1016/j.tibs.2004.11.008openalex-snapshot
Protein folding and the organization of the protein topology universe
inferredcites →https://doi.org/10.1016/s0022-2836(03)00028-7openalex-snapshot
Rapid Cooperative Two-state Folding of a Miniature α–β Protein and Design of a Thermostable Variant
inferredcites →https://doi.org/10.1016/s0022-2836(03)00616-8openalex-snapshot
NMR and Temperature-jump Measurements of de Novo Designed Proteins Demonstrate Rapid Folding in the Absence of Explicit Selection for Kinetics
inferredcites →https://doi.org/10.1016/s0959-440x(98)80012-2openalex-snapshot
Pathways for protein folding: is a new view needed?
inferredcites →https://doi.org/10.1017/s0033583508004654openalex-snapshot
Protein folding and misfolding: mechanism and principles
inferredcites →https://doi.org/10.1021/ja8030533openalex-snapshot
Crystal Structure of a Ten-Amino Acid Protein
inferredcites →https://doi.org/10.1021/jp049652qopenalex-snapshot
Folding of A Three-Helix Bundle at the Folding Speed Limit
inferredcites →https://doi.org/10.1021/jp0757715openalex-snapshot
Estimating Free-Energy Barrier Heights for an Ultrafast Folding Protein from Calorimetric and Kinetic Data
inferredcites →https://doi.org/10.1021/jp110738mopenalex-snapshot
Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch?
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1038/77971openalex-snapshot
Critical role of beta-hairpin formation in protein G folding.
inferredcites →https://doi.org/10.1038/89638openalex-snapshot
Computer-based redesign of a protein folding pathway.
inferredcites →https://doi.org/10.1038/nphys1713openalex-snapshot
Challenges in protein-folding simulations
inferredcites →https://doi.org/10.1038/nsb794openalex-snapshot
Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects
inferredcites →https://doi.org/10.1038/nsb947openalex-snapshot
Parallel protein-unfolding pathways revealed and mapped
inferredcites →https://doi.org/10.1038/nsmb765openalex-snapshot
Transition states for protein folding have native topologies despite high structural variability
inferredcites →https://doi.org/10.1063/1.1630572openalex-snapshot
From transition paths to transition states and rate coefficients
inferredcites →https://doi.org/10.1063/1.1839571openalex-snapshot
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
inferredcites →https://doi.org/10.1063/1.2206581openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.3077008openalex-snapshot
A one-dimensional free energy surface does not account for two-probe folding kinetics of protein α3D
inferredcites →https://doi.org/10.1063/1.440484openalex-snapshot
The stable states picture of chemical reactions. I. Formulation for rate constants and initial condition effects
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.447334openalex-snapshot
A unified formulation of the constant temperature molecular dynamics methods
inferredcites →https://doi.org/10.1063/1.463940openalex-snapshot
Nosé–Hoover chains: The canonical ensemble via continuous dynamics
inferredcites →https://doi.org/10.1073/pnas.0408098102openalex-snapshot
Reaction coordinates and rates from transition paths
inferredcites →https://doi.org/10.1073/pnas.2136623100openalex-snapshot
Ultrafast folding of α 3 D: A de novo designed three-helix bundle protein
inferredcites →https://doi.org/10.1073/pnas.242424399openalex-snapshot
A self-organizing principle for learning nonlinear manifolds
inferredcites →https://doi.org/10.1073/pnas.92.24.10869openalex-snapshot
Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.
inferredcites →https://doi.org/10.1073/pnas.96.10.5486openalex-snapshot
Solution structure and dynamics of a de novo designed three-helix bundle protein
inferredcites →https://doi.org/10.1088/0953-8984/17/18/010openalex-snapshot
Evaluating protein structure descriptors and tuning Gauss integral based descriptors
inferredcites →https://doi.org/10.1093/bioinformatics/btl332openalex-snapshot
THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
inferredcites →https://doi.org/10.1093/protein/gzm082openalex-snapshot
The Trp-cage: optimizing the stability of a globular miniprotein
inferredcites →https://doi.org/10.1103/physreva.31.1695openalex-snapshot
Canonical dynamics: Equilibrium phase-space distributions
inferredcites →https://doi.org/10.1109/arith.2009.33openalex-snapshot
Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins
inferredcites →https://doi.org/10.1110/ps.036319.108openalex-snapshot
Kinetic barriers and the role of topology in protein and RNA folding
inferredcites →https://doi.org/10.1110/ps.051856406openalex-snapshot
Methionine oxidation of monomeric λ repressor: The denatured state ensemble under nondenaturing conditions
inferredcites →https://doi.org/10.1126/science.1136800openalex-snapshot
Clustering by Passing Messages Between Data Points
inferredcites →https://doi.org/10.1126/science.1187409openalex-snapshot
Atomic-Level Characterization of the Structural Dynamics of Proteins
inferredcites →https://doi.org/10.1145/1188455.1188544openalex-snapshot
Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters
inferredcites →https://doi.org/10.1145/1654059.1654099openalex-snapshot
Millisecond-scale molecular dynamics simulations on Anton
inferredcites →https://doi.org/10.1371/journal.pone.0018868openalex-snapshot
The Energy Computation Paradox and ab initio Protein Folding
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inferred← citeshttps://doi.org/10.1002/1873-3468.12098openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1873-3468.12836openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118468654.ch2openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118681121.ch22openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118845226.ch6openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118866641.ch18openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118889886.ch1openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118889886.ch3openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781119085126.ch15openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781119855668.ch7openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781394236145.ch8openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527697106.ch17openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adma.201304475openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adma.201800701openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adts.201800171openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adts.201800175openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.201403924openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.201502938openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.202505971openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.201309174openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.201403924openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.201502938openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.202505971openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/bip.22355openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/bip.22640openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cem.70097openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.27026openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.27059openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2065openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2081openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2335openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2433openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2727openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2738openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2797openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.2922openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.3015openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.3238openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.3914openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4096openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4905openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.5205openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.5219openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.70073openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.70107openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.70354openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.70794openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.24068openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.24098openalex-snapshot
Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/prot.24109openalex-snapshot
Sequential four‐state folding/unfolding of goat α‐lactalbumin and its N‐terminal variants
inferred← citeshttps://doi.org/10.1002/prot.24175openalex-snapshot
Separability between overall and internal motion: A protein folding problem
inferred← citeshttps://doi.org/10.1002/prot.24269openalex-snapshot
Folding and stability of helical bundle proteins from coarse‐grained models
inferred← citeshttps://doi.org/10.1002/prot.24295openalex-snapshot
Folding of Top7 in unbiased all‐atom Monte Carlo simulations
inferred← citeshttps://doi.org/10.1002/prot.24301openalex-snapshot
Right‐ and left‐handed three‐helix proteins. I. Experimental and simulation analysis of differences in folding and structure
inferred← citeshttps://doi.org/10.1002/prot.24319openalex-snapshot
Ab initio folding of extended α‐helix: A theoretical study about the role of electrostatic polarization in the folding of helical structures
inferred← citeshttps://doi.org/10.1002/prot.24386openalex-snapshot
Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method
inferred← citeshttps://doi.org/10.1002/prot.24416openalex-snapshot
Folding 19 proteins to their native state and stability of large proteins from a coarse‐grained model
inferred← citeshttps://doi.org/10.1002/prot.24483openalex-snapshot
Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure
inferred← citeshttps://doi.org/10.1002/prot.24613openalex-snapshot
A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability
inferred← citeshttps://doi.org/10.1002/prot.24633openalex-snapshot
Extracting representative structures from protein conformational ensembles
inferred← citeshttps://doi.org/10.1002/prot.24695openalex-snapshot
Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/prot.24759openalex-snapshot
Evaluation of conformational changes in diabetes‐associated mutation in insulin a chain: A molecular dynamics study
inferred← citeshttps://doi.org/10.1002/prot.24846openalex-snapshot
Protein structure refinement by optimization
inferred← citeshttps://doi.org/10.1002/prot.24852openalex-snapshot
Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics
inferred← citeshttps://doi.org/10.1002/prot.24871openalex-snapshot
Protein structure refinement via molecular‐dynamics simulations: What works and what does not?
inferred← citeshttps://doi.org/10.1002/prot.24947openalex-snapshot
Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics
inferred← citeshttps://doi.org/10.1002/prot.25011openalex-snapshot
A hidden aggregation‐prone structure in the heart of hypoxia inducible factor prolyl hydroxylase
inferred← citeshttps://doi.org/10.1002/prot.25030openalex-snapshot
Protein side chain conformation predictions with an MMGBSA energy function
inferred← citeshttps://doi.org/10.1002/prot.25094openalex-snapshot
FF12MC: A revised AMBER forcefield and new protein simulation protocol
inferred← citeshttps://doi.org/10.1002/prot.25157openalex-snapshot
Temperature-induced unfolding behavior of proteins studied by tensorial elastic network model
inferred← citeshttps://doi.org/10.1002/prot.25266openalex-snapshot
Experimental conformational energy maps of proteins and peptides
inferred← citeshttps://doi.org/10.1002/prot.25367openalex-snapshot
Protein structure prediction: making AWSEM AWSEM‐ER by adding evolutionary restraints
inferred← citeshttps://doi.org/10.1002/prot.25409openalex-snapshot
Assessment of the model refinement category in CASP12
inferred← citeshttps://doi.org/10.1002/prot.25439openalex-snapshot
Effects of force fields on the conformational and dynamic properties of amyloid β(1‐40) dimer explored by replica exchange molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/prot.25812openalex-snapshot
Novel phosphorylation‐dependent regulation in an unstructured protein
inferred← citeshttps://doi.org/10.1002/prot.25897openalex-snapshot
Common mechanism of thermostability in small α‐ and β‐proteins studied by molecular dynamics
inferred← citeshttps://doi.org/10.1002/prot.26062openalex-snapshot
Investigating the folding mechanism of the N‐terminal domain of ribosomal protein L9
inferred← citeshttps://doi.org/10.1002/prot.26154openalex-snapshot
Entropy‐based distance cutoff for protein internal contact networks
inferred← citeshttps://doi.org/10.1002/prot.26478openalex-snapshot
Protein structure prediction using the evolutionary algorithm USPEX
inferred← citeshttps://doi.org/10.1002/prot.26479openalex-snapshot
Functional, pathogenic, and pharmacological roles of protein folding intermediates
inferred← citeshttps://doi.org/10.1002/qua.24785openalex-snapshot
REIN: Replica‐exchange INterface for simulating protein dynamics and function
inferred← citeshttps://doi.org/10.1002/qua.24841openalex-snapshot
MODYLAS: A highly parallelized general‐purpose molecular dynamics simulation program
inferred← citeshttps://doi.org/10.1002/qua.26984openalex-snapshot
Machine learning of atomic forces from quantum mechanics: An approach based on pairwise interatomic forces
inferred← citeshttps://doi.org/10.1002/qub2.70024openalex-snapshot
Advances and challenges in multiscale biomolecular simulations: artificial intelligence‐driven paradigm shift
inferred← citeshttps://doi.org/10.1002/slct.201903633openalex-snapshot
Fullerene Stability by Geometrical Thermodynamics
inferred← citeshttps://doi.org/10.1002/solr.202000352openalex-snapshot
Mesoscale Simulations on Morphology Design in Conjugated Polymers and Inorganic Nanoparticles Composite for Bulk Heterojunction Solar Cells
inferred← citeshttps://doi.org/10.1002/wcms.1133openalex-snapshot
Coarse‐grained models of protein folding as detailed tools to connect with experiments
inferred← citeshttps://doi.org/10.1002/wcms.1167openalex-snapshot
Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation
inferred← citeshttps://doi.org/10.1002/wcms.1169openalex-snapshot
The power of coarse graining in biomolecular simulations
inferred← citeshttps://doi.org/10.1002/wcms.1306openalex-snapshot
Molecular ‘time‐machines’ to unravel key biological events for drug design
inferred← citeshttps://doi.org/10.1002/wcms.1307openalex-snapshot
Computational protein structure refinement: almost there, yet still so far to go
inferred← citeshttps://doi.org/10.1002/wcms.1309openalex-snapshot
Accelerating physical simulations of proteins by leveraging external knowledge
inferred← citeshttps://doi.org/10.1002/wcms.1347openalex-snapshot
Water models for biomolecular simulations
inferred← citeshttps://doi.org/10.1002/wcms.1449openalex-snapshot
Surviving the deluge of biosimulation data
inferred← citeshttps://doi.org/10.1002/wcms.1560openalex-snapshot
Quantitative predictions from molecular simulations using explicit or implicit interactions
inferred← citeshttps://doi.org/10.1002/wcms.1578openalex-snapshot
How to strike a conformational balance in protein force fields for molecular dynamics simulations?
inferred← citeshttps://doi.org/10.1002/wcms.70064openalex-snapshot
Breaking the Barriers of Molecular Dynamics With Deep‐Learning: Opportunities, Pitfalls, and How to Navigate Them
inferred← citeshttps://doi.org/10.1002/wrna.1396openalex-snapshot
Advances in RNA molecular dynamics: a simulator's guide to RNA force fields
inferred← citeshttps://doi.org/10.1007/10_2021_189openalex-snapshot
Evolution of Artificial Intelligence-Powered Technologies in Biomedical Research and Healthcare
inferred← citeshttps://doi.org/10.1007/7653_2015_47openalex-snapshot
A Review of Evolutionary Algorithms for Computing Functional Conformations of Protein Molecules
inferred← citeshttps://doi.org/10.1007/7653_2015_58openalex-snapshot
Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-1-0716-1716-8_18openalex-snapshot
Atomistic Simulations of Thermal Unfolding
inferred← citeshttps://doi.org/10.1007/978-1-0716-1716-8_19openalex-snapshot
Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms
inferred← citeshttps://doi.org/10.1007/978-1-0716-2974-1_2openalex-snapshot
Illuminating the “Twilight Zone”: Advances in Difficult Protein Modeling
inferred← citeshttps://doi.org/10.1007/978-1-0716-3441-7_7openalex-snapshot
Applications of Molecular Dynamics Simulations in Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-1-0716-3565-0_12openalex-snapshot
Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods
inferred← citeshttps://doi.org/10.1007/978-1-4614-2146-7_2openalex-snapshot
The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules
inferred← citeshttps://doi.org/10.1007/978-1-4939-0366-5_16openalex-snapshot
Protocols for Efficient Simulations of Long-Time Protein Dynamics Using Coarse-Grained CABS Model
inferred← citeshttps://doi.org/10.1007/978-1-4939-0667-3_9-1openalex-snapshot
Substrate-Envelope-Guided Design of Drugs with a High Barrier to the Evolution of Resistance
inferred← citeshttps://doi.org/10.1007/978-1-4939-0694-9_9openalex-snapshot
Substrate-Envelope-Guided Design of Drugs with a High Barrier to the Evolution of Resistance
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_12openalex-snapshot
Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_7openalex-snapshot
Coarse-Grained Force Fields for Molecular Simulations
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_8openalex-snapshot
Tackling Sampling Challenges in Biomolecular Simulations
inferred← citeshttps://doi.org/10.1007/978-1-4939-2285-7_1openalex-snapshot
De Novo Peptide Structure Prediction: An Overview
inferred← citeshttps://doi.org/10.1007/978-1-4939-6406-2_8openalex-snapshot
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model
inferred← citeshttps://doi.org/10.1007/978-1-4939-6637-0_5openalex-snapshot
Geometric Potentials for Computational Protein Sequence Design
inferred← citeshttps://doi.org/10.1007/978-1-4939-9121-1_2openalex-snapshot
Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs
inferred← citeshttps://doi.org/10.1007/978-1-4939-9608-7_1openalex-snapshot
Atomistic Force Fields for Proteins
inferred← citeshttps://doi.org/10.1007/978-3-030-13325-2_4openalex-snapshot
Interactions Between Blood Proteins and Nanoparticles Investigated Using Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1007/978-3-030-16443-0_10openalex-snapshot
Applications of Molecular Dynamics Simulations in Computational Toxicology
inferred← citeshttps://doi.org/10.1007/978-3-030-40245-7_16openalex-snapshot
Machine Learning for Molecular Dynamics on Long Timescales
inferred← citeshttps://doi.org/10.1007/978-3-030-80602-6_3openalex-snapshot
Atomistic Simulations of the Human Proteasome Inhibited by a Covalent Ligand
inferred← citeshttps://doi.org/10.1007/978-3-030-80924-9_1openalex-snapshot
Water Contribution to the Protein Folding and Its Relevance in Protein Design and Protein Aggregation
inferred← citeshttps://doi.org/10.1007/978-3-030-94651-7_7openalex-snapshot
Molecular Dynamics Simulations: Concept, Methods, and Applications
inferred← citeshttps://doi.org/10.1007/978-3-030-98606-3_2openalex-snapshot
Probing the Energy Landscapes of Biomolecular Folding and Function
inferred← citeshttps://doi.org/10.1007/978-3-030-98606-3_3openalex-snapshot
Energetic and Structural Properties of Macromolecular Assemblies
inferred← citeshttps://doi.org/10.1007/978-3-031-42999-6_3openalex-snapshot
Enzyme Modeling: From the Sequence to the Substrate Complex
inferred← citeshttps://doi.org/10.1007/978-3-031-47303-6_12openalex-snapshot
Applications of Ab Initio Molecular Dynamics for Modeling Batteries
inferred← citeshttps://doi.org/10.1007/978-3-031-67802-8_2openalex-snapshot
Concentration of Empirical First-Passage Times
inferred← citeshttps://doi.org/10.1007/978-3-031-76718-0_14openalex-snapshot
Exploring the Significance of Experimental and Computational Methods in Protein Structure Determination
inferred← citeshttps://doi.org/10.1007/978-3-319-13521-2_24openalex-snapshot
Molecular Dynamics Simulations to Study Structure-Function Relationship in Psychrophilic Enzymes
inferred← citeshttps://doi.org/10.1007/978-3-319-14929-5_11openalex-snapshot
Probing Microsecond Reactions with Microfluidic Mixers and TCSPC
inferred← citeshttps://doi.org/10.1007/978-3-319-72218-4_1openalex-snapshot
Protein Folding in Vivo: From Anfinsen Back to Levinthal
inferred← citeshttps://doi.org/10.1007/978-3-319-73441-5_56openalex-snapshot
Sampling in In Silico Biomolecular Studies: Single-Stage Experiments vs Multiscale Approaches
inferred← citeshttps://doi.org/10.1007/978-3-319-95843-9_4openalex-snapshot
Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field
inferred← citeshttps://doi.org/10.1007/978-3-319-95843-9_8openalex-snapshot
Enhanced Sampling for Biomolecular Simulations
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