2018
July: De Novo Designed Alpha-Sheet Peptides Inhibit Functional Amyloid Formation of Streptococcus Mutans Biofilms [DOI]
September: Molecular dynamics-derived rotamer libraries for D-amino acids within homochiral and heterochiral polypeptides [DOI]
October Protein engineering reveals mechanisms of functional amyloid formation in Pseudomonas aeruginosa biofilms [DOI]
2012
January: GB1 Is Not a Two-State Folder: Identification and Characterization of an On-Pathway Intermediate [DOI]
April: A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8 [DOI]
June: Disruption of the X-loop turn of the prion protein linked to scrapie resistance [DOI]
July: A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations [DOI]
August: Structural and Functional Consequences of the Cardiac Troponin C L48Q Ca2+-Sensitizing Mutation [DOI]
September: Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain [DOI]
2011
January: Generation of a consensus protein domain dictionary [DOI]
February: The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water [DOI]
March: The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function [DOI]
May: Manifestations of Native Topology in the Denatured State Ensemble of Rhodopseudomonas palustris Cytochrome c′ [DOI]
June: Structural Effects of the L145Q, V157F, and R282W Cancer-Associated Mutations in the p53 DNA-Binding Core Domain [DOI]
July: Malleability of folding intermediates in the homeodomain superfamily [DOI]
August: Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection [DOI]
October: The effect of context on the folding of β-hairpins [DOI]
November: Protein simulation data in the relational model [DOI]
December: A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8 [DOI]
2010
January: The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures [DOI]
February: Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold [DOI]
April: Dynameomics: A Comprehensive Database of Protein Dynamics [DOI]
June: Polymorphisms and disease: hotspots of inactivation in methyltransferases [DOI]
July: A Comprehensive Multidimensional-Embedded, One-Dimensional Reaction Coordinate for Protein Unfolding/Folding [DOI]
September: Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate [DOI]
November: The influence of pH on the human prion protein: Insights into the early steps of misfolding [DOI]
December: Diverse Effects on the Native β-Sheet of the Human Prion Protein Due to Disease-Associated Mutations [DOI]
2009
January: Species variation in PrPSc protofibril models [DOI]
March: Characterization of cell-surface prion protein relative to its recombinant analogue: insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein [DOI]
June: A Hotspot of Inactivation: The A22S and V108M Polymorphisms Individually Destabilize the Active Site Structure of Catechol O-Methyltransferase [DOI]
July: The R46Q, R131Q and R154H Polymorphs of Human DNA Glycosylase/β-Lyase hOgg1 Severely Distort the Active Site and DNA Recognition Site but do not Cause Unfolding [DOI]
August: The consequences of pathogenic mutations to the human prion protein [DOI]
September: Structural Changes to Monomeric CuZn Superoxide Dismutase Caused by the Familial Amyotrophic Lateral Sclerosis-Associated Mutation A4V [DOI]
October: The V119I Polymorphism in Protein L-Isoaspartate O-Methyltransferase Alters the Substrate-Binding Interface [DOI]
November: Principles of Ligand Binding within a Completely Buried Cavity in HIF2α PAS-B [DOI]
December: Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds [DOI]
2008
January: Conformational Changes below the Tm: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A [DOI]
February: The Histamine N-Methyltransferase T105I Polymorphism Affects Active Site Structure and Dynamics [DOI]
March: Combining experiment and simulation in protein folding: closing the gap for small model systems [DOI]
April: Different disease-causing mutations in transthyretin trigger the same conformational conversion [DOI]
May: Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations [DOI]
June: Four Human Thiopurine S-Methyltransferase Alleles Severely Affect Protein Structure and Dynamics [DOI]
July: Side-chain dynamics are critical for water permeation through aquaporin-1 [DOI]
August: Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain [DOI]
September: The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins [DOI]
October: Molecular Basis for the Structural Instability of Human DJ-1 Induced by the L166P Mutation Associated with Parkinson's Disease [DOI]
November: Dynameomics: Large-Scale Assessment of Native Protein Flexibility [DOI]
December: The V108M mutation decreases the structural stability of catechol O-methyltransferase [DOI]
2007
January: Structural Properties of Prion Protein Protofibrils and Fibrils: An Experimental Assessment of Atomic Models [DOI]
February: Folding mechanisms of proteins with high sequence identity but different folds [DOI]
March: Direct Observation of Microscopic Reversibility in Single-molecule Protein Folding [DOI]
April: Conformational Entropy of Alanine versus Glycine in Protein Denatured States [DOI]
May: Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations [DOI]
October: The role of the turn in β-hairpin formation during WW domain folding [DOI]
November: Simulations of Macromolecules in Protective and Denaturing Osmolytes: Properties of Mixed Solvent Systems and Their Effects on Water and Protein Structure and Dynamics [DOI]
December: A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent Pfold-Like Calculations [HTML]
2006
January: Local environmental effects on the structure of the prion protein [DOI]
February: Characterization of Two Distinct β2-Microglobulin Unfolding Intermediates that May Lead to Amyloid Fibrils of Different Morphology [DOI]
March: The 108M Polymorph of Human Catechol O-Methyltransferase Is Prone to Deformation at Physiological Temperatures [DOI]
April: Importance of Context in Protein Folding: Secondary Structural Propensities versus Tertiary Contact-Assisted Secondary Structure Formation [DOI]
May: The Folding Pathway of Spectrin R17 from Experiment and Simulations: Using Experimentally Validated MD Simulations to Characterize States Hinted at by Experiment [DOI]
June: Protein Folding-Simulation [DOI]
July: Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation [DOI]
September: α-Sheet: The toxic conformer in amyloid diseases? [DOI]
2005
October: Characterization of a possible amyloidogenic precursor in glutamine-repeat diseases [DOI]
November: Ensemble versus single-molecule protein unfolding [DOI]
December: Cutoff size need not strongly influence molecular dynamics results on solvated polypeptides [DOI]
