J. Straub

发表

On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters

I. Andricioaei, J. Straub, 1997 .

Development of novel statistical potentials for protein fold recognition.

D Thirumalai, N-V Buchete, J E Straub, 2004, Current opinion in structural biology.

Molecular dynamics study of an isomerizing diatomic in a Lennard‐Jones fluid

B. Berne, J. Straub, M. Borkovec, 1988 .

Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models.

J. Straub, Jaegil Kim, T. Keyes, 2007, The Journal of chemical physics.

Replica exchange statistical temperature molecular dynamics algorithm.

J. Straub, Jaegil Kim, T. Keyes, 2012, The journal of physical chemistry. B.

Statistical-temperature Monte Carlo and molecular dynamics algorithms.

J. Straub, Jaegil Kim, T. Keyes, 2006, Physical review letters.

Generalized parallel sampling

J. Straub, T. Whitfield, L. Bu, 2002 .

Smart Darting Monte Carlo

A. Voter, I. Andricioaei, J. Straub, 2001 .

Novel methods of sampling phase space in the simulation of biological systems.

B. Berne, J. Straub, 1997, Current opinion in structural biology.

The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature

J. Straub, S. Huo, Shuanghong Huo, 1997 .

Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant.

J. Straub, D. Klimov, D. Thirumalai, 2002, Protein science : a publication of the Protein Society.

Charge states rather than propensity for β‐structure determine enhanced fibrillogenesis in wild‐type Alzheimer's β‐amyloid peptide compared to E22Q Dutch mutant

J. Straub, D. Klimov, D. Thirumalai, 2002 .

Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution.

J. Straub, F. Massi, J. Peng, 2001, Biophysical journal.

Optimal replica exchange method combined with Tsallis weight sampling.

J. Straub, Jaegil Kim, 2009, The Journal of chemical physics.

Replica exchange statistical temperature Monte Carlo.

John E Straub, J. Straub, Jaegil Kim, 2009, The Journal of chemical physics.

Enhanced sampling in numerical path integration: an approximation for the quantum statistical density matrix based on the nonextensive thermostatistics.

J. Straub, T. Whitfield, 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials.

John E Straub, J. Straub, Alan E van Giessen, 2005, The Journal of chemical physics.

Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis.

D Thirumalai, J. Straub, N. Buchete, 2004, Journal of molecular graphics & modelling.

Orientational potentials extracted from protein structures improve native fold recognition

J. Straub, N. Buchete, D. Thirumalai, 2004, Protein science : a publication of the Protein Society.

Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures

D. Thirumalai, J. Straub, N. Buchete, 2003, physics/0302009.

Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: Application to enhanced equilibrium averaging and global optimization

J. Straub, Jianpeng Ma, D. Hsu, 1993 .

Proteins : energy, heat and signal flow

J. Straub, D. Leitner, 2009 .

Molecular dynamics simulation of NO recombination to myoglobin mutants.

J. Straub, R. Elber, H. Li, 1993, The Journal of biological chemistry.

Toward a molecular theory of early and late events in monomer to amyloid fibril formation.

J. Straub, D. Thirumalai, 2011, Annual review of physical chemistry.

Generalized simulated tempering for exploring strong phase transitions.

J. Straub, Jaegil Kim, 2010, The Journal of chemical physics.

Role of water in protein aggregation and amyloid polymorphism.

John E Straub, Govardhan Reddy, J. Straub, 2011, Accounts of chemical research.

Mode-specific vibrational energy relaxation of amide I' and II' modes in N-methylacetamide/water clusters: intra- and intermolecular energy transfer mechanisms.

J. Straub, Yong Zhang, H. Fujisaki, 2009, The journal of physical chemistry. A.

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation

George A. Pantelopulos, J. Straub, 2018 .

Spatio-temporal hierarchy in the dynamics of a minimalist protein model.

J. Straub, R. Berry, Chun-Biu Li, 2013, The Journal of chemical physics.

Global energy minimum searches using an approximate solution of the imaginary time Schroedinger equation

J. Straub, P. Amara, D. Hsu, 1993 .

Global optimization using bad derivatives: Derivative‐free method for molecular energy minimization

I. Andricioaei, J. Straub, 1998 .

Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation

Jianpeng Ma, John E. Straub, Patricia Amara, 1995 .

Simulated annealing using the classical density distribution

Jianpeng Ma, John E. Straub, J. Straub, 1994 .

Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides.

J. Straub, M. Grinstaff, C. McKnight, 2016, Journal of the American Chemical Society.

Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways

B. Reinhard, J. Straub, Tom Keyes, 2018, Proceedings of the National Academy of Sciences.

Ergodic Problems for Real Complex Systems in Chemical Physics

J. Straub, R. Berry, T. Komatsuzaki, 2011 .

Freezing Transitions of Nanoconfined Coarse-Grained Water Show Subtle Dependence on Confining Environment.

J. Straub, Qing Lu, 2016, The journal of physical chemistry. B.

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

J. Straub, Jaegil Kim, Qing Lu, 2013, The Journal of chemical physics.

Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins.

J. Straub, D. Thirumalai, Pavel I Zhuravlev, 2014, Journal of molecular biology.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00980a Click here for additional data file.

J. Straub, L. Domínguez, R. Aguayo-Ortiz, 2017, Chemical science.

Coarse-Grained Model of Coil-to-Helix Kinetics Demonstrates the Importance of Multiple Nucleation Sites in Helix Folding.

J. Straub, Alan E van Giessen, Alan E. van Giessen, 2006, Journal of chemical theory and computation.

On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions

J. Straub, N. Buchete, D. Thirumalai, 2008 .

Reaction Rates and Transition Pathways

J. Straub, 2001 .

Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides.

J. Straub, M. Grinstaff, Hannah E Caputo, 2019, Chemical Society reviews.

Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing.

John E Straub, J. Straub, Jaegil Kim, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins.

J. Straub, D. Thirumalai, Debayan Chakraborty, 2019, The journal of physical chemistry. B.

Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

J. Straub, D. Thirumalai, Debayan Chakraborty, 2018, bioRxiv.

Microgravity Evaluation of Colorimetric-Solid Phase Extraction for the Measurement of Total I (Iodine, Iodide, and Triiodide) in Spacecraft Drinking Water

J. Straub, D. Gazda, M. Porter, 2008 .

MOLECULAR DYNAMICS SIMULATION STUDY OF THE B-STATES OF SOLVATED CARBON MONOXYMYOGLOBIN

J. Straub, Jianpeng Ma, Shuanghong Huo, 1997 .

Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A.

J. Straub, O. Gursky, M. Fändrich, 2020, Journal of molecular biology.

Dynamics of methionine ligand rebinding in cytochrome c.

J. Straub, E. Malolepsza, Ping Zhang, 2012, The journal of physical chemistry. B.

Vibrational energy relaxation in proteins.

J. Straub, H. Fujisaki, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles.

J. Straub, Qing Lu, E. Malolepsza, 2014, The Journal of chemical physics.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.

Son Tung Ngo, Bikash R. Sahoo, R. Nussinov, 2021, Chemical reviews.

Cellular prion protein targets amyloid-β fibril ends via its C-terminal domain to prevent elongation

J. Straub, D. Harris, Ryo Urano, 2017, The Journal of Biological Chemistry.

On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.

J. Straub, Ayan Majumder, Seulki Kwon, 2022, Journal of chemical theory and computation.

Finite-Size Effects and Optimal System Sizes in Simulations of Surfactant Micelle Self-Assembly.

George A. Pantelopulos, J. Straub, Jonathan J W Harris, 2020, The journal of physical chemistry. B.

Direct Observation of Cholesterol Dimers and Tetramers in Lipid Bilayers.

George A. Pantelopulos, J. Straub, M. Hong, 2021, The journal of physical chemistry. B.

2020 JCP Emerging Investigator Special Collection.

J. Straub, D. Reichman, A. Michaelides, 2021, The Journal of chemical physics.

Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model.

J. Straub, Ayan Majumder, 2021, Journal of chemical theory and computation.

Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations

J. Straub, E. Malolepsza, 2014, The journal of physical chemistry. B.

Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers.

J. Straub, D. Thirumalai, B. Tarus, 2006, Journal of the American Chemical Society.

Aqueous urea solution destabilizes Abeta(16-22) oligomers.

J. Straub, D. Klimov, D. Thirumalai, 2004, Proceedings of the National Academy of Sciences of the United States of America.

JCP Emerging Investigator Special Collection 2019.

J. Straub, D. Reichman, T. Martínez, 2020, The Journal of chemical physics.

Characterization of dynamics and mechanism in the self-assembly of AOT reverse micelles.

George A. Pantelopulos, J. Straub, Shanshan Song, 2018, The Journal of chemical physics.

A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin.

J. Straub, D. Sagnella, 1999, Biophysical Journal.

Simulation study of the collapse of linear and ring homopolymers

J. Straub, E. Shakhnovich, Jianpeng Ma, 1995 .

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Carlos R. Baiz, J. Straub, J. Hirst, 2020, Chemical reviews.

Probing the structure and dynamics of confined water in AOT reverse micelles.

J. Straub, Adam Moser, L. Domínguez, 2013, The journal of physical chemistry. B.

Quantum and classical vibrational relaxation dynamics of N‐methylacetamide on ab initio potential energy surfaces

J. Straub, K. Hirao, G. Stock, 2008, 0807.1368.

Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin : ligand dynamics in the first 10 ps

M. Karplus, J. Straub, 1991 .

Protein folding in a reverse micelle environment: the role of confinement and dehydration.

J. Straub, L. Domínguez, Susan C. Desensi, 2011, The Journal of chemical physics.

Non‐Markovian Theory of Vibrational Energy Relaxation and its Applications to Biomolecular Systems

J. Straub, Yong Zhang, H. Fujisaki, 2010, 1003.4796.

Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide.

J. Straub, D. Thirumalai, E. Rivera, 2009, Biophysical journal.

Aerosol-OT Surfactant Forms Stable Reverse Micelles in Apolar Solvent in the Absence of Water

George A. Pantelopulos, J. Straub, Ryo Urano, 2019 .

Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method

J. Straub, K. Hirao, H. Fujisaki, 2007, 0706.1905.

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation

George A. Pantelopulos, J. Straub, 2018, bioRxiv.

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The nu(4) and nu(7) modes of nonplanar nickel porphyrin models.

J. Straub, Yong Zhang, 2009, The Journal of chemical physics.

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The nu(4) and nu(7) modes of iron-protoporphyrin IX and iron porphine.

J. Straub, Yong Zhang, 2009, The Journal of chemical physics.

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model.

J. Straub, Yong Zhang, H. Fujisaki, 2009, The Journal of chemical physics.

Theoretical Study of Intramultiplet Transitions in Collisions of Atoms in (3)P Electronic States with Structureless Targets: Ca((3)P)+He,

J. Straub, M. Alexander, T. Orlikowski, 1983 .

Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C.

John E Straub, J. Straub, L. Bu, 2003, Biophysical journal.

Vibrational energy relaxation (VER) of a CD stretching mode in cytochrome c

J. Straub, L. Bu, H. Fujisaki, 2004, q-bio/0403019.

Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants.

J. Straub, D. Thirumalai, Debayan Chakraborty, 2021, The journal of physical chemistry letters.

Sequence Determines the Switch in the Fibril Forming Regions in the Low Complexity FUS Protein and Its Variants

J. Straub, D. Thirumalai, Debayan Chakraborty, 2021, bioRxiv.

Aqueous urea solution destabilizes Aβ16–22 oligomers

J. Straub, D. Thirumalai, D. Klimov, 2004 .

Classical and modern methods in reaction rate theory

John E. Straub, Bruce J. Berne, Michal Borkovec, 1988 .

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities

J. Straub, D. Thirumalai, Debayan Chakraborty, 2020, Proceedings of the National Academy of Sciences.

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their distinct aggregation propensities

J. Straub, D. Thirumalai, Debayan Chakraborty, 2020, bioRxiv.

Conformational Fluctuations and Phases in Fused in Sarcoma (FUS) Low-Complexity Domain.

J. Straub, D. Thirumalai, Debayan Chakraborty, 2023, ArXiv.

Resilience of the iron environment in heme proteins.

John E Straub, Jiyong Zhao, J. Straub, 2008, Biophysical journal.

Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles

J. Straub, L. Domínguez, Qing Lu, 2014, The journal of physical chemistry. B.

Energy landscape theory for Alzheimer's amyloid β‐peptide fibril elongation

Francesca Massi, J. Straub, F. Massi, 2001 .

Energy landscape theory for Alzheimer's amyloid beta-peptide fibril elongation.

J. Straub, F. Massi, 2001, Proteins.

Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature.

J. Straub, D. Thirumalai, L. Domínguez, 2014, Journal of the American Chemical Society.

Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase.

John E. Straub, Naoyuki Miyashita, D. Thirumalai, 2009, Journal of the American Chemical Society.

Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein

J. Straub, D. Thirumalai, L. Domínguez, 2016, Proceedings of the National Academy of Sciences.

Probing the origins of increased activity of the E22Q "Dutch" mutant Alzheimer's beta-amyloid peptide.

J. Straub, F. Massi, J E Straub, 2001, Biophysical journal.

Molecular basis for a novel systemic form of human hereditary apoA-I amyloidosis with vision loss

J. Straub, N. Rioux-Leclercq, F. Paraf, 2018, bioRxiv.

Molecular Insights into Human Hereditary Apolipoprotein A-I Amyloidosis Caused by the Glu34Lys Mutation.

J. Straub, O. Gursky, I. Morgado, 2018, Biochemistry.

Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization.

D Thirumalai, John E Straub, J. Straub, 2005, Journal of molecular biology.

Structure of APP-C991-99 and Implications for Role of Extra-Membrane Domains in Function and Oligomerization

George A. Pantelopulos, Y. Sugita, J. Straub, 2018, bioRxiv.

A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization.

J. Straub, G. Bitan, D. Teplow, 2003, Journal of the American Chemical Society.

Impact of Cholesterol Concentration and Lipid Phase on Structure and Fluctuation of Amyloid Precursor Protein.

George A. Pantelopulos, J. Straub, Afra Panahi, 2020, The journal of physical chemistry. B.

IV. ComputationalMetho ds for the Simulation of Classical and Quantum Many Body Systems Arising from Nonextensive Thermostatistics

I. Andricioaei, J. Straub, 2001 .

Probing vibrational energy relaxation in proteins using normal modes

J. Straub, L. Bu, H. Fujisaki, 2004, q-bio/0408023.

Structure of APP-C991-99 and Implications for Role of Extra-Membrane Domains in Function and Oligomerization

George A. Pantelopulos, Y. Sugita, J. Straub, 2018, bioRxiv.

Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures.

Asanga Bandara, Afra Panahi, George A Pantelopulos, 2017, The Journal of chemical physics.

Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture.

George A. Pantelopulos, J. Straub, T. Nagai, 2019, The Journal of chemical physics.

Probing the mechanisms of fibril formation using lattice models.

D Thirumalai, Mai Suan Li, J. Straub, 2008, The Journal of chemical physics.

Uncertainty of path integral averages at low temperature

J. Straub, T. Whitfield, 2001 .

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins.

J. Straub, Yong Zhang, H. Fujisaki, 2006, The Journal of chemical physics.

Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins.

George A. Pantelopulos, Kathleen F. Mittendorf, J. Straub, 2020, Journal of the American Chemical Society.

Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein.

George A. Pantelopulos, J. Straub, L. Domínguez, 2016, The journal of physical chemistry letters.

Spatial dependence of time‐dependent friction for pair diffusion in a simple fluid

B. Berne, J. Straub, B. Roux, 1990 .

Calculation of dynamic friction on intramolecular degrees of freedom

B. Berne, J. Straub, M. Borkovec, 1987 .

On determining reaction kinetics by molecular dynamics using absorbing barriers

B. Berne, J. Straub, D. Hsu, 1985 .

Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations.

J. Straub, M. Lim, P. Anfinrud, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Dynamic friction on rigid and flexible bonds

John E. Straub, Mark E. Tuckerman, Bruce J. Berne, 1990 .

Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation.

J. Straub, D. Thirumalai, G. Reddy, 2009, The journal of physical chemistry. B.

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide.

Bernard R Brooks, John E Straub, Edward P O'Brien, 2011, The journal of physical chemistry letters.

New and notable: A multiscale coarse-grained model of the SARS-CoV-2 virion

John E. Straub, J. Straub, 2021, Biophysical Journal.

Gravitational smoothing as a global optimization strategy

John E. Straub, T. W. Whitfield, J. Straub, 2002, J. Comput. Chem..

Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles

B. Reinhard, J. Straub, Zhiliang He, 2021, Proceedings of the National Academy of Sciences.

Efficient calculation of the free energy for protein partitioning using restraining potentials.

George A. Pantelopulos, J. Straub, Seulki Kwon, 2022, Biophysical journal.

Entropic stabilization of proteins by TMAO.

Samuel S. Cho, J. Straub, D. Thirumalai, 2011, The journal of physical chemistry. B.

Freezing Transitions of Nanocon fi ned Coarse-Grained Water Show Subtle Dependence on Con fi ning Environment

J. Straub, Qing Lu, 2016 .

Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization

Ron Elber, John E Straub, Shruthi Viswanath, 2015, Proteins.

Structural Heterogeneity in Transmembrane Amyloid Precursor Protein Homodimer Is a Consequence of Environmental Selection

John E. Straub, Leigh Foster, Laura Dominguez, 2014, Journal of the American Chemical Society.

Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations.

D Thirumalai, Yuji Sugita, John E Straub, 2009, Journal of the American Chemical Society.

Sizes, conformational fluctuations, and SAXS profiles for Intrinsically Disordered Proteins

J. Straub, D. Thirumalai, Debayan Chakraborty, 2024, bioRxiv.

Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald’s rule of stages

J. Straub, D. Thirumalai, Debayan Chakraborty, 2022, bioRxiv.

Factors governing fibrillogenesis of polypeptide chains revealed by lattice models.

D Thirumalai, Chin-Kun Hu, Mai Suan Li, 2010, Physical review letters.

Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions.

D Thirumalai, John E Straub, J. Straub, 2008, Journal of molecular biology.

Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism

D Thirumalai, Gerhard Stock, Mai Suan Li, 2007, Proceedings of the National Academy of Sciences.

Protein Folding and Optimization Algorithms

John E. Straub, J. Straub, 2002 .

Simulation of quantum systems using path integrals in a generalized ensemble

M. Karplus, I. Andricioaei, J. Straub, 2001 .

FOLDING MODEL PROTEINS USING KINETIC AND THERMODYNAMIC ANNEALING OF THE CLASSICAL DENSITY DISTRIBUTION

John E. Straub, Patricia Amara, J. Straub, 1995 .

Dynamics of locking of peptides onto growing amyloid fibrils

J. Straub, D. Thirumalai, G. Reddy, 2009, Proceedings of the National Academy of Sciences.

Principles governing oligomer formation in amyloidogenic peptides.

John E Straub, J. Straub, D. Thirumalai, 2010, Current opinion in structural biology.

Generalized replica exchange method.

John E Straub, J. Straub, Jaegil Kim, 2010, The Journal of chemical physics.

Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces

J. Straub, D. Leitner, Yao Xu, 2014, Theoretical Chemistry Accounts.

Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin.

J. Straub, Yong Zhang, H. Fujisaki, 2007, The journal of physical chemistry. B.

Diversity of solvent dependent energy transfer pathways in heme proteins.

J. Straub, Yong Zhang, 2009, The journal of physical chemistry. B.

Efforts toward developing direct probes of protein dynamics.

J. Straub, P. Dawson, F. Romesberg, 2006, Journal of the American Chemical Society.

Vibrational Energy Relaxation of “Tailored” Hemes in Myoglobin Following Ligand Photolysis Supports Energy Funneling Mechanism of Heme “Cooling”

J. Straub, Lintao Bu and, 2003 .

Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin

John E. Straub, J. Straub, D. Thirumalai, 2000 .

Influence of membrane lipid composition on the structure and activity of γ-secretase.

J. Straub, L. Domínguez, R. Aguayo‐Ortiz, 2018, Physical chemistry chemical physics : PCCP.

Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A

D. Thirumalai, J. Straub, D. Thirumalai, 1994 .

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

Yuko Okamoto, Bernard R Brooks, John E Straub, 2009, The journal of physical chemistry. B.

Exploring the energy landscape in proteins.

D Thirumalai, J. Straub, D. Thirumalai, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: theoretical investigation of vibrational energy relaxation rates and pathways.

J. Straub, H. Fujisaki, 2007, The journal of physical chemistry. B.

Directed Energy "Funneling" Mechanism for Heme Cooling Following Ligand Photolysis or Direct Excitation in Solvated Carbonmonoxy Myoglobin

J. Straub, Diane E. Sagnella and, 2001 .

Membrane-protein interactions hold the key to understanding amyloid formation

J. Straub, D. Thirumalai, 2014, 1407.1713.

Membrane-Protein Interactions Are Key to Understanding Amyloid Formation.

J. Straub, D. Thirumalai, 2014, The journal of physical chemistry letters.

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.

D. Wales, J. Straub, Jaegil Kim, 2014, The Journal of chemical physics.

A statistical theory for the effect of nonadiabatic transitions on activated processes

B. Berne, J. Straub, 1987 .

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires

J. Straub, D. Thirumalai, G. Reddy, 2010, Proceedings of the National Academy of Sciences.

Simulating vibrational energy flow in proteins: Relaxation rate and mechanism for heme cooling in cytochrome c

John E. Straub, J. Straub, L. Bu, 2003 .

Analysis of the role of attractive forces in self-diffusion of a simple fluid

J. Straub, 1992 .

Limit of metastability for liquid and vapor phases of water.

Woo Jong Cho, J. Straub, Joonho Lee, 2014, Physical review letters.

Exploring the solid-liquid phase change of an adapted Dzugutov model using generalized replica exchange method.

John E Straub, J. Straub, Jaegil Kim, 2012, The journal of physical chemistry. B.

Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables.

J. Straub, Jaegil Kim, T. Keyes, 2011, The Journal of chemical physics.

Structural and dynamical analysis of the hydration of the Alzheimer's β‐amyloid peptide

Francesca Massi, John E. Straub, J. Straub, 2003, J. Comput. Chem..

Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99

George A. Pantelopulos, Y. Sugita, J. Straub, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Finding the needle in the haystack: algorithms for conformational optimization

John E. Straub, Ioan Adricioaei, J. Straub, 1996 .

Relationship between protein folding thermodynamics and the energy landscape.

J. Straub, Jaegil Kim, T. Keyes, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c: Theoretical investigation of VER rates and pathways

J. Straub, H. Fujisaki, 2007, 0707.2300.

Molecular Insights into Human Hereditary Apolipoprotein A ‐ I Amyloidosis Caused by the Glu 34 Lys Mutation

J. Straub, O. Gursky, I. Morgado, 2018 .

Direct computation of long time processes in peptides and proteins: Reaction path study of the coil‐to‐helix transition in polyalanine

J. Straub, J E Straub, S Huo, 1999, Proteins.

Long time dynamic simulations: exploring the folding pathways of an Alzheimer's amyloid Abeta-peptide.

J. Straub, Jonathan P. Lee, Shuanghong Huo, 2002, Accounts of chemical research.

A rapid method for determining rate constants by molecular dynamics

B. Berne, J. Straub, 1985 .

Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain.

J. Straub, D. Thirumalai, Debayan Chakraborty, 2023, Biopolymers.

Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble

J. Straub, B. Imperiali, Ayan Majumder, 2023, bioRxiv.

Aerosol-OT Surfactant Forms Stable Reverse Micelles in Apolar Solvent in the Absence of Water.

George A. Pantelopulos, J. Straub, Ryo Urano, 2018, The journal of physical chemistry. B.

Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy.

J. Straub, A. Palmer, Meiling Zhang, 2021, Biophysicist.

Microgravity Evaluation of Colorimetric-Solid Phase Extraction for the Measurement of Total I in Spacecraft Drinking Water

J. Straub, D. Gazda, M. Porter, 2010 .

APC mutations in sporadic colorectal tumors: A mutational "hotspot" and interdependence of the "two hits".

J Straub, W F Bodmer, J. Straub, 2000, Proceedings of the National Academy of Sciences of the United States of America.

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Takuya Takahashi, John E. Straub, Tetsuro Nagai, 2016, J. Comput. Chem..

dock-lock mechanism Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage

J. Straub, D. Thirumalai, P. Nguyen, 2007 .

The influence of intramolecular vibrational relaxation on the pressure dependence of unimolecular rate constants

B. Berne, J. Straub, M. Borkovec, 1986 .

Conformational Fluctuations and Phases in Fused in Sarcoma (FUS) Low-Complexity Domain

J. Straub, D. Thirumalai, Debayan Chakraborty, 2023, ArXiv.

Mean First-Passage Time Calculations for the Coil-to-Helix Transition: The Active Helix Ising Model†

J. Straub, Nicolae-Viorel Buchete and, 2001 .

Charge states rather than propensity for β‐structure determine enhanced fibrillogenesis in wild‐type Alzheimer's β‐amyloid peptide compared to E22Q Dutch mutant

J. Straub, D. Klimov, D. Thirumalai, 2002 .

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires

H. Scheraga, J. Straub, D. Thirumalai, 2010, Proceedings of the National Academy of Sciences.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model.

J. Straub, Chun-Biu Li, T. Komatsuzaki, 2013, The Journal of chemical physics.

Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture.

George A. Pantelopulos, J. Straub, T. Nagai, 2019, The Journal of chemical physics.

Influence of membrane lipid composition on the structure and activity of γ-secretase.

J. Straub, L. Domínguez, R. Aguayo‐Ortiz, 2018, Physical chemistry chemical physics : PCCP.

Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers

John E. Straub, Asanga Bandara, Afra Panahi, 2017, J. Comput. Chem..

An efficient Monte Carlo algorithm for overcoming broken ergodicity in the simulation of spin systems

I. Andricioaei, J. Straub, 1997 .

Theoretical probes of conformational fluctuations in S‐peptide and RNase A/3′–UMP enzyme product complex

J. Straub, D. Thirumalai, D. Thirumalai2, 1993, Proteins.

Erratum: Simulated annealing using the classical density distribution [J. Chem. Phys. 101, 533 (1994)]

Jianpeng Ma, John E. Straub, J. Straub, 1995 .

"Strange kinetics" in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c.

J. Straub, Ping Zhang, Steven Ahn, 2013, The journal of physical chemistry. B.

Dynamics of methionine ligand rebinding in cytochrome c.

J. Straub, E. Malolepsza, Ping Zhang, 2012, The journal of physical chemistry. B.

Non‐Markovian activated rate processes: Comparison of current theories with numerical simulation data

B. Berne, J. Straub, M. Borkovec, 1986 .

Numerical simulation of rate constants for a two degree of freedom system in the weak collision limit

B. Berne, J. Straub, M. Borkovec, 1987 .

Energy diffusion in many‐dimensional Markovian systems: The consequences of competition between inter‐ and intramolecular vibrational energy transfer

B. Berne, J. Straub, 1986 .

Shortcomings of current theories of non‐Markovian activated rate processes

B. Berne, J. Straub, M. Borkovec, 1985 .

Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide.

J. Straub, D. Thirumalai, E. Rivera, 2009, Biophysical journal.

Potable Water Quality for International Space Station Expeditions 30-33

John E. Straub, John R. Schultz, Debrah K. Plumlee, 2013 .

ISS Expeditions 16 Thru 20: Chemical Analysis Results for Potable Water

John E. Straub, John R. Schultz, Debrah K. Plumlee, 2013 .

Chemical Analysis Results for Potable Water from ISS Expeditions 21 through 25

John E. Straub, John R. Schultz, J. Torin McCoy, 2011 .

Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases

John E. Straub, Nicolae-Viorel Buchete, J. Straub, 2004 .