Carlos Simmerling

National Research University Higher School of Economics

Also affiliated with Lomonosov Moscow State University, Stony Brook University

Biochemistry, Genetics and Molecular BiologyMaterials ScienceMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 7%percentile

0.165Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions

International Journal of Molecular Sciences(2022)10.3390/ijms232315371

Top 70%

0.165DataRank

Top 70%2 citations

Sandi Brudar, Evangelos A. Coutsias, Ken A. Dill, Miha Lukšič, Carlos Simmerling +2 more

Papers

Driven by 33 papers — median percentile 30. Top paper: “ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB”.

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

Journal of Chemical Theory and Computation(2015)10.1021/acs.jctc.5b00255

N/A

1.4DataRank · unranked

10859 citations

Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, Carlos Simmerling +3 more

The Amber biomolecular simulation programs

Journal of Computational Chemistry(2005)10.1002/jcc.20290

N/A

1.4DataRank · unranked

9524 citations

Thomas E. Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz +6 more

Copper stabilizes antiparallel β-sheet fibrils of the amyloid β40 (Aβ40)-Iowa variant

Journal of Biological Chemistry(2020)10.1074/jbc.ra119.011955

N/A

0.479DataRank · unranked

11 citations

Brandon A. Irizarry, Martine Ziliox, Toru Kawakami, Tiffany W. Victor, Feng Xu +7 more

InSty: A ProDy Module for Evaluating Protein Interactions and Stability

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169009

N/A

0.269DataRank · unranked

5 citations

James Krieger, Anupam Banerjee, Xin Cao, Gary D. Wu, Anthony T. Bogetti +5 more

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions

International Journal of Molecular Sciences(2022)10.3390/ijms232315371

Top 70%

0.165DataRank

Top 70%2 citations

Sandi Brudar, Evangelos A. Coutsias, Ken A. Dill, Miha Lukšič, Carlos Simmerling +2 more

The flexibility of ACE2 in the context of SARS-CoV-2 infection

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.16.300459

N/A

0DataRank · unranked

19 citations

Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, Yanbin Wang, Lucy Fallon +5 more

Free Energy Landscapes for RBD Opening in SARS-CoV-2 Spike Glycoprotein Simulations Suggest Key Interactions and a Potentially Druggable Allosteric Pocket

ChemRxiv(2020)10.26434/chemrxiv.13502646.v1

N/A

0DataRank · unranked

9 citations

Kellon Belfon, Lauren Raguette, Yuzhang Wang, Christopher Corbo, Darya Stepanenko +7 more

Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.29.925040

N/A

0DataRank · unranked

2 citations

Jinnette Tolentino Collado, Agnieszka A. Gil, Pavithran T. Ravindran, András Lukács, SeungYoun Shin +16 more

Free Energy Landscapes for RBD Opening in SARS-CoV-2 Spike Glycoprotein Simulations Suggest Key Interactions and a Potentially Druggable Allosteric Pocket

ChemRxiv(2020)10.26434/chemrxiv.13502646

N/A

0DataRank · unranked

1 citations

Kellon Belfon, Lauren Raguette, Yuzhang Wang, Christopher Corbo, Darya Stepanenko +7 more

Exploring Protocols to Build Reservoirs to Accelerate Replica Exchange MD Simulations

ChemRxiv(2020)10.26434/chemrxiv.12328007

N/A

0DataRank · unranked

0 citations

kenneth lam, Carlos Simmerling, Koushik Kasavajhala

Exploring Protocols to Build Reservoirs to Accelerate Replica Exchange MD Simulations

ChemRxiv(2020)10.26434/chemrxiv.12328007.v1

N/A

0DataRank · unranked

0 citations

kenneth lam, Carlos Simmerling, Koushik Kasavajhala

GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses

ACS Central Science(2021)10.1021/acscentsci.1c01080

N/A

0DataRank · unranked

52 citations

Fiona L. Kearns, Mia A. Rosenfeld, Lorenzo Casalino, Micah J. Papanikolas, Carlos Simmerling +3 more

Receptor binding may directly activate the fusion machinery in coronavirus spike glycoproteins

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.10.443496

N/A

0DataRank · unranked

5 citations

Lucy Fallon, Lauren Raguette, Stephanie Budhan, Kellon Belfon, Darya Stepanenko +4 more

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

ChemRxiv(2021)10.26434/chemrxiv.14140790

N/A

0DataRank · unranked

2 citations

Zhipeng Li, Shuai Liu, Chunwang Peng, Dong Fang, Xiao Wan +6 more

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

ChemRxiv(2021)10.26434/chemrxiv.14140790.v1

N/A

0DataRank · unranked

1 citations

Zhipeng Li, Shuai Liu, Chunwang Peng, Dong Fang, Xiao Wan +6 more

Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir

Journal of Chemical Theory and Computation(2022)10.1021/acs.jctc.2c00065

N/A

0DataRank · unranked

11 citations

Koushik Kasavajhala, Sarah Gunasekera, Carlos Simmerling, kenneth lam

On the plasticity of amyloid formation: The impact of destabilizing small to large substitutions on islet amyloid polypeptide amyloid formation

Protein Science(2022)10.1002/pro.4539

N/A

0DataRank · unranked

4 citations

Rehana Akter, Alexander Zhyvoloup, Carlos Simmerling, Daniel P. Raleigh, Lakshan Manathunga

AmberTools

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01153

N/A

0DataRank · unranked

1916 citations

Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro +42 more

Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00005

N/A

0DataRank · unranked

4 citations

Carlos Simmerling, Koushik Kasavajhala

Rapid Rescoring and Refinement of Ligand–Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00345

N/A

0DataRank · unranked

1 citations

Kelley Chiu, John D. Bickel, Robert C. Rizzo, Carlos Simmerling, Juan Alcantara

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.29.569310

N/A

0DataRank · unranked

11 citations

Dmytro Kalitin, Darya Stepanenko, Y. Zhu, Thu Nguyen, George Jones +7 more

Rapid rescoring and refinement of ligand-receptor complexes using REMD with a MC pose reservoir

ChemRxiv(2023)10.26434/chemrxiv-2023-pkdm3

N/A

0DataRank · unranked

1 citations

Kelley Chiu, John D. Bickel, Robert C. Rizzo, Carlos Simmerling, Juan Alcantara

k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00308

N/A

0DataRank · unranked

39 citations

Daniel R. Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda‐Quintana, Lexin Chen

MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction

Biophysical Journal(2024)10.1016/j.bpj.2024.05.011

N/A

0DataRank · unranked

17 citations

Dmytro Kalitin, Darya Stepanenko, Y. Zhu, Thu Nguyen, George Jones +8 more

Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.3c01366

N/A

0DataRank · unranked

8 citations

Michelle Hummel, Yuzhang Wang, Carlos Simmerling, Evangelos A. Coutsias, Xin Cao

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c00756

N/A

0DataRank · unranked

4 citations

Ethan Aminov, Aalim S. Abdullah, Colleen Kirkup, Rebeca I. Diaz Ventura, Vinay R. Bijoor +19 more

Phospho-Tune: Enhanced Structural Modeling of Phosphorylated Protein Interactions

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.29.582580

N/A

0DataRank · unranked

7 citations

Veranika Averkava, Sergei Kotelnikov, Darya Stepanenko, Thu Nguyen, Julie C. Mitchell +6 more

k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.07.583975

N/A

0DataRank · unranked

3 citations

Daniel R. Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda‐Quintana, Lexin Chen

Adjusting the energy profile for CH–O interactions leads to improved stability of RNA stem-loop structures in MD simulations

ChemRxiv(2024)10.26434/chemrxiv-2024-9rbjw

N/A

0DataRank · unranked

3 citations

Sarah Gunasekera, Rebeca I. Diaz Ventura, Ethan Aminov, Jason Linzer, Diksha Parwana +4 more

Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs

PubMed(2024)10.48550/arxiv.2401.10462

N/A

0DataRank · unranked

0 citations

Michelle Hummel, Yuzhang Wang, Carlos Simmerling, Evangelos A. Coutsias, Xin Cao

Recent Developments in Amber Biomolecular Simulations

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c01063

N/A

0DataRank · unranked

131 citations

David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed +26 more

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.19.390187

N/A

0DataRank · unranked

46 citations

Abigail C. Dommer, Zied Gaieb, Emília P. Barros, Terra Sztain, Surl-Hee Ahn +23 more

The flexibility of ACE2 in the context of SARS-CoV-2 infection

Biophysical Journal(2020)10.1016/j.bpj.2020.10.036

N/A

0DataRank · unranked

136 citations

Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, Yuzhang Wang, Lucy Fallon +5 more

Carlos Simmerling

Indexed papers

Top data-sharing exemplar

Papers