Skip to content

Home Search Authors Pakistan News Saved

SciRah

SciRah does not host or store research papers. Results come live from free, official scholarly APIs, and every paper links back to its original source.

Data sources

OpenAlex
Semantic Scholar
Crossref
CORE
arXiv
PubMed

Privacy policy Terms of service

P. Maragakis · SciRah

Researcher profile · Semantic Scholar

P. Maragakis

Share profile

P. Maragakis — researcher profile on SciRah

h-index: 30
Works: 47
Citations: 12K

Most-cited papers

Improved side-chain torsion potentials for the Amber ff99SB protein force field
K. Lindorff-Larsen, S. Piana, Kim Palmo, P. Maragakis +3 more
2010Proteins: Structure, Function, and Bioinformatics5,989 citations Open access
Semantic Scholar
Atomic-Level Characterization of the Structural Dynamics of Proteins
D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana +7 more
2010Science1,298 citations
Semantic Scholar
Pathway and mechanism of drug binding to G-protein-coupled receptors
R. Dror, Albert C. Pan, D. Arlow, D. Borhani +4 more
2011Proceedings of the National Academy of Sciences of the United States of America724 citations Open access
Semantic Scholar
Systematic Validation of Protein Force Fields against Experimental Data
K. Lindorff-Larsen, P. Maragakis, S. Piana, M. Eastwood +2 more
2012PLoS ONE664 citations Open access
Semantic Scholar
Activation mechanism of the β2-adrenergic receptor
R. Dror, D. Arlow, P. Maragakis, Thomas J. Mildorf +4 more
2011Proceedings of the National Academy of Sciences of the United States of America614 citations Open access
Semantic Scholar
Millisecond-scale molecular dynamics simulations on Anton
D. E. Shaw, R. Dror, J. Salmon, J. P. Grossman +18 more
2009Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis449 citations
Semantic Scholar
Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.
P. Maragakis, M. Karplus
2005Journal of Molecular Biology317 citations
Semantic Scholar
Principles of conduction and hydrophobic gating in K+ channels
M. Jensen, D. Borhani, K. Lindorff-Larsen, P. Maragakis +4 more
2010Proceedings of the National Academy of Sciences of the United States of America309 citations Open access
Semantic Scholar
Structure and dynamics of an unfolded protein examined by molecular dynamics simulation.
K. Lindorff-Larsen, N. Trbovic, P. Maragakis, S. Piana +1 more
2012Journal of the American Chemical Society241 citations
Semantic Scholar
Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.
Wei-Qing Ren, E. Vanden-Eijnden, P. Maragakis, W. E
2005Journal of Chemical Physics205 citations
Semantic Scholar
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.
P. Maragakis, K. Lindorff-Larsen, M. Eastwood, R. Dror +8 more
2008Journal of Physical Chemistry B186 citations Open access
Semantic Scholar
Adaptive nudged elastic band approach for transition state calculation
P. Maragakis, S. Andreev, Yisroel Brumer, D. Reichman +1 more
2002179 citations Open access
Semantic Scholar
DNA nucleoside interaction and identification with carbon nanotubes.
Sheng Meng, P. Maragakis, C. Papaloukas, E. Kaxiras
2007Nano letters (Print)147 citations
Semantic Scholar
Carbon nanotube interaction with DNA.
G. Lu, P. Maragakis, E. Kaxiras
2005Nano letters (Print)135 citations
Semantic Scholar
Two-electron atoms in strong fields
P. Lambropoulos, P. Maragakis, Jian Zhang
1998122 citations
Semantic Scholar
Picosecond to Millisecond Structural Dynamics in Human Ubiquitin.
K. Lindorff-Larsen, P. Maragakis, S. Piana, D. E. Shaw
2016Journal of Physical Chemistry B115 citations Open access
Semantic Scholar
Millisecond-scale molecular dynamics simulations on Anton
D. E. Shaw, R. Dror, J. Salmon, J. P. Grossman +18 more
2009Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis114 citations
Semantic Scholar
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
T. Tu, C. Rendleman, D. Borhani, R. Dror +7 more
20082008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis80 citations
Semantic Scholar
Gaussian-mixture umbrella sampling
P. Maragakis, A. van der Vaart, M. Karplus
2009Journal of Physical Chemistry B65 citations Open access
Semantic Scholar
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.
P. Maragakis, F. Ritort, C. Bustamante, M. Karplus +1 more
2007Journal of Chemical Physics63 citations Open access
Semantic Scholar
Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance.
Sheng Meng, Wei-Li Wang, P. Maragakis, E. Kaxiras
2007Nano letters (Print)52 citations Open access
Semantic Scholar
Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.
W. Wriggers, Kate A. Stafford, Y. Shan, S. Piana +8 more
2009Journal of Chemical Theory and Computation50 citations
Semantic Scholar
Optimal estimates of free energies from multistate nonequilibrium work data.
P. Maragakis, Martin Spichty, M. Karplus
2006Physical Review Letters49 citations Open access
Semantic Scholar
Equipartition and the Calculation of Temperature in Biomolecular Simulations.
M. Eastwood, Kate A. Stafford, R. Lippert, M. Jensen +4 more
2010Journal of Chemical Theory and Computation45 citations Open access
Semantic Scholar
Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors.
Alexander M. Taylor, Bret R Williams, Fabrizio Giordanetto, Elizabeth H Kelley +33 more
2023Journal of Medicinal Chemistry41 citations Open access
Semantic Scholar
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography
J. Greisman, Lindsay Willmore, Christine Y Yeh, F. Giordanetto +4 more
2023Journal of Chemical Information and Modeling36 citations Open access
Semantic Scholar
A deep-learning view of chemical space designed to facilitate drug discovery
P. Maragakis, Hunter M. Nisonoff, B. Cole, D. E. Shaw
2020Journal of Chemical Information and Modeling36 citations Open access
Semantic Scholar
A differential fluctuation theorem.
P. Maragakis, Martin Spichty, M. Karplus
2008Journal of Physical Chemistry B31 citations
Semantic Scholar
ACRES: An Efficient Method for First-Principles Electronic Structure Calculations of Complex Systems
U. Waghmare, Hanchul Kim, I. Park, N. Modine +2 more
200031 citations Open access
Semantic Scholar
Electronic structure of overstretched DNA
P. Maragakis, R. Barnett, E. Kaxiras, M. Elstner +1 more
200230 citations Open access
Semantic Scholar
Multiphoton ionization saturation intensities and generalized cross sections from ATI spectra
D. Charalambidis, D. Xenakis, C. Uiterwaal, P. Maragakis +4 more
199725 citations
Semantic Scholar
Generalized multiphoton-ionization cross sections of the rare gases for 500-fs, 248.6-nm pulses
C. Uiterwaal, D. Xenakis, D. Charalambidis, P. Maragakis +2 more
199821 citations
Semantic Scholar
A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis
Christine Y Yeh, J. Izaguirre, J. Greisman, Lindsay Willmore +2 more
2020bioRxiv16 citations Open access
Semantic Scholar
Time-dependent calculation of ionization in potassium at midinfrared wavelengths
P. Maragakis, É. Cormier, P. Lambropoulos
19996 citations Open access
Semantic Scholar
Theory of laser-induced two-step electron-ion recombination
P. Schlagheck, P. Maragakis, P. Lambropoulos
19966 citations
Semantic Scholar
Abstract 3327: Discovery and characterization of the potent, allosteric SHP2 inhibitor GDC-1971 for the treatment of RTK/RAS driven tumors
Bret R Williams, A. Taylor, Olivia Orozco, Christopher Owen +34 more
2022Cancer Research5 citations
Semantic Scholar
Correction: Systematic Validation of Protein Force Fields against Experimental Data
K. Lindorff-Larsen, P. Maragakis, S. Piana, M. Eastwood +2 more
2013PLoS ONE5 citations Open access
Semantic Scholar
Automated Event Detection and Activity Monitoring in Long Time-Scale Molecular Dynamics
W. Wriggers, Kate A. Stafford, Y. Shan, Stefano Piana-Agostinetti +6 more
20095 citations Open access
Semantic Scholar
Improving Molecular Mechanics Force Fields By Comparison Of Microsecond Simulations With Nmr Experiments
Stefano Piana-Agostinetti, K. Lindorff-Larsen, P. Maragakis, M. Eastwood +2 more
20093 citations Open access
Semantic Scholar
Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography
J. Greisman, Lindsay Willmore, Christine Y Yeh, F. Giordanetto +4 more
2023bioRxiv2 citations Open access
Semantic Scholar
Multiscale model of electronic behavior and localization in stretched dry DNA
R. Barnett, P. Maragakis, A. Turner, M. Fyta +1 more
20072 citations Open access
Semantic Scholar
Erratum: Optimal Estimates of Free Energies from Multistate Nonequilibrium Work Data [Phys. Rev. Lett. 96, 100602 (2006)]
P. Maragakis, Martin Spichty, M. Karplus
20071 citations Open access
Semantic Scholar
Gradual broadening of successive above-threshold-ionization peaks
L. Nikolopoulos, P. Maragakis
20011 citations
Semantic Scholar
Permeation And Conformational Changes Of The Pore Domain Of The Kv1.2 Potassium Channel
M. Jensen, D. Borhani, R. Dror, M. Eastwood +3 more
20090 citations Open access
Semantic Scholar
Pentacene Molecules on Inert Surfaces
Yina Mo, P. Maragakis, E. Kaxiras
20070 citations
Semantic Scholar
Time-dependent calculations in Potassium: mid-infrared wavelengths
P. Maragakis, É. Cormier, P. Lambropoulos
19990 citations
Semantic Scholar
Multiphoton ionization saturation intensities and generalized cross sections from ATI spectra
D. Charalambidis, D. Xenakis, C. Uiterwaal, P. Maragakis +4 more
19970 citations
Semantic Scholar

Frequent co-authors

Invite them to SciRah by sharing their profile.

D. E. Shaw×22
Invite
D. E. Shaw — researcher profile on SciRah
R. Dror×16
Invite
R. Dror — researcher profile on SciRah
K. Lindorff-Larsen×14
Invite
K. Lindorff-Larsen — researcher profile on SciRah
M. Eastwood×12
Invite
M. Eastwood — researcher profile on SciRah

×9

Invite

S. Piana — researcher profile on SciRah

Invite

E. Kaxiras — researcher profile on SciRah

P. Lambropoulos×7

Invite

P. Lambropoulos — researcher profile on SciRah

Invite

Y. Shan — researcher profile on SciRah

Invite

M. Karplus — researcher profile on SciRah

Invite

J. Klepeis — researcher profile on SciRah

Invite

D. Borhani — researcher profile on SciRah

Invite

M. Jensen — researcher profile on SciRah