P. Maragakis

发表

Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, J. A. Bank, R. Dror, 2022 .

Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance.

E. Kaxiras, P. Maragakis, S. Meng, 2007, Nano letters.

Improved side-chain torsion potentials for the Amber ff99SB protein force field

R. Dror, K. Lindorff-Larsen, D. Shaw, 2010, Proteins.

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.

R. Dror, R. Friesner, K. Lindorff-Larsen, 2008, The journal of physical chemistry. B.

Systematic Validation of Protein Force Fields against Experimental Data

R. Dror, K. Lindorff-Larsen, D. Shaw, 2012, PloS one.

Pathway and mechanism of drug binding to G-protein-coupled receptors

Albert C. Pan, R. Dror, D. Shaw, 2011, Proceedings of the National Academy of Sciences.

Activation mechanism of the β2-adrenergic receptor

Albert C. Pan, R. Dror, D. Shaw, 2011, Proceedings of the National Academy of Sciences.

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin.

K. Lindorff-Larsen, D. Shaw, P. Maragakis, 2016, The journal of physical chemistry. B.

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation.

K. Lindorff-Larsen, D. Shaw, P. Maragakis, 2012, Journal of the American Chemical Society.

Improving Molecular Mechanics Force Fields By Comparison Of Microsecond Simulations With Nmr Experiments

R. Dror, K. Lindorff-Larsen, D. Shaw, 2009 .

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.

Martin Karplus, Paul Maragakis, M. Karplus, 2005, Journal of molecular biology.

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

John L. Klepeis, David E. Shaw, Charles A. Rendleman, 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

Millisecond-scale molecular dynamics simulations on Anton

J. P. Grossman, Joseph A. Bank, Martin M. Deneroff, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

O ct 2 00 2 Electronic structure of overstretched DNA

E. Kaxiras, P. Maragakis, M. Elstner, 2017 .

Millisecond-scale molecular dynamics simulations on Anton

J. P. Grossman, Joseph A. Bank, Martin M. Deneroff, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

ACRES: An Efficient Method for First-Principles Electronic Structure Calculations of Complex Systems

E. Kaxiras, Hanchul Kim, P. Maragakis, 2000, cond-mat/0006183.

Electronic structure of overstretched DNA The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters

E. Kaxiras, P. Maragakis, M. Elstner, 2017 .

Optimal estimates of free energies from multistate nonequilibrium work data.

M. Karplus, P. Maragakis, M. Spichty, 2006, Physical review letters.

Multiscale model of electronic behavior and localization in stretched dry DNA

E. Kaxiras, P. Maragakis, A. Turner, 2007, 0704.0660.

Time-dependent calculation of ionization in potassium at midinfrared wavelengths

P. Maragakis, É. Cormier, P. Lambropoulos, 1999, physics/9904053.

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Martin Karplus, Carlos Bustamante, Paul Maragakis, 2007, The Journal of chemical physics.

Multiphoton ionization saturation intensities and generalized cross sections from ATI spectra

P. Maragakis, H. Schröder, O. Faucher, 1997 .

Two-electron atoms in strong fields

P. Maragakis, P. Lambropoulos, Jian Zhang, 1998 .

A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis

D. Shaw, P. Maragakis, J. Izaguirre, 2020, bioRxiv.

Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography

Hunter M Nisonoff, Hunter M. Nisonoff, D. Shaw, 2023, bioRxiv.

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.

Eric Vanden-Eijnden, Weiqing Ren, Weinan E, 2005, The Journal of chemical physics.

Carbon nanotube interaction with DNA.

Efthimios Kaxiras, Gang Lu, Paul Maragakis, 2005, Nano letters.

Adaptive nudged elastic band approach for transition state calculation

Efthimios Kaxiras, David R. Reichman, Paul Maragakis, 2002 .

Principles of conduction and hydrophobic gating in K+ channels

Kresten Lindorff-Larsen, Michael P Eastwood, Ron O Dror, 2010, Proceedings of the National Academy of Sciences.

Theory of laser-induced two-step electron-ion recombination

P. Maragakis, P. Schlagheck, P. Lambropoulos, 1996 .

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

John L. Klepeis, David E. Shaw, Ron O. Dror, 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

Gaussian-mixture umbrella sampling.

Martin Karplus, Paul Maragakis, M. Karplus, 2009, The journal of physical chemistry. B.

A deep-learning view of chemical space designed to facilitate drug discovery

David E. Shaw, Brian Cole, Hunter M. Nisonoff, 2020, J. Chem. Inf. Model..

DNA nucleoside interaction and identification with carbon nanotubes.

E. Kaxiras, P. Maragakis, S. Meng, 2007, Nano letters.

Abstract 3327: Discovery and characterization of the potent, allosteric SHP2 inhibitor GDC-1971 for the treatment of RTK/RAS driven tumors

D. Bergstrom, M. Murcko, D. Shaw, 2022, Cancer Research.

Electronic structure of overstretched DNA

E. Kaxiras, P. Maragakis, M. Elstner, 2002, cond-mat/0210663.

Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography

Hunter M. Nisonoff, D. Shaw, P. Maragakis, 2023, J. Chem. Inf. Model..