Carlos L Simmerling (Carlos Simmerling)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 48

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

International journal of molecular sciences

bioRxiv : the preprint server for biology

Stony Brook University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Stony Brook University Aug 15 1998

United States

Professor :: Chemistry

Publications

Lauren E Raguette, Sarah S Gunasekera, Rebeca I Diaz Ventura, Ethan Aminov, Jason T Linzer, Diksha Parwana, Qin Wu, Carlos L Simmerling, Maria C Nagan
Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations. The journal of physical chemistry. B (2024)
Jason T Linzer, Ethan Aminov, Aalim S Abdullah, Colleen E Kirkup, Rebeca I Diaz Ventura, Vinay R Bijoor, Jiyun Jung, Sophie Huang, Chi Gee Tse, Emily Álvarez Toucet, Hugo P Onghai, Arghya Pratim Ghosh, Alex C Grodzki, Emilee R Haines, Aditya S Iyer, Mark K Khalil, Alexander P Leong, Michael A Neuhaus, Joseph Park, Asir Shahid, Matthew Xie, Jan M Ziembicki, Carlos L Simmerling, Maria C Nagan
Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. Journal of chemical information and modeling (2024)
Lauren E Raguette, Abbigayle E Cuomo, Kellon A A Belfon, Chuan Tian, Victoria Hazoglou, Gabriela Witek, Stephen M Telehany, Qin Wu, Carlos L Simmerling
phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids. Journal of chemical theory and computation (2024)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. bioRxiv : the preprint server for biology (2024)
Darya Stepanenko, Yuzhang Wang, Carlos L Simmerling
Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein. Viruses 16 (7) (2024)
Xin Cao, Michelle H Hummel, Yuzhang Wang, Carlos L Simmerling, Evangelos A Coutsias
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)
Jason T Linzer, Ethan Aminov, Aalim S Abdullah, Colleen E Kirkup, Rebeca I Diaz Ventura, Vinay R Bijoor, Jiyun Jung, Sophie Huang, Chi Gee Tse, Emily Álvarez Toucet, Hugo P Onghai, Arghya Pratim Ghosh, Alex C Grodzki, Emilee R Haines, Aditya S Iyer, Mark K Khalil, Alexander P Leong, Michael A Neuhaus, Joseph Park, Asir Shahid, Matthew Xie, Jan M Ziembicki, Carlos L Simmerling, Maria C Nagan
Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. Journal of chemical information and modeling 64 (15) (2024)
Xin Cao, Michelle H Hummel, Yuzhang Wang, Carlos L Simmerling, Evangelos A Coutsias
Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs. Journal of chemical theory and computation 20 (11) (2024)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (13) (2024)
Lauren E Raguette, Sarah S Gunasekera, Rebeca I Diaz Ventura, Ethan Aminov, Jason T Linzer, Diksha Parwana, Qin Wu, Carlos L Simmerling, Maria C Nagan
Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations. The journal of physical chemistry. B 128 (33) (2024)
Darya Stepanenko, Yuzhang Wang, Carlos L Simmerling
Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein. Viruses 16 (7) (2024)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. bioRxiv : the preprint server for biology (2024)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. bioRxiv : the preprint server for biology (2024)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations. Journal of chemical theory and computation (2024)
Xin Cao, Michelle H Hummel, Yuzhang Wang, Carlos L Simmerling, Evangelos A Coutsias
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)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. bioRxiv : the preprint server for biology (2024)
Darya Stepanenko, Yuzhang Wang, Carlos L Simmerling
Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein. Viruses 16 (7) (2024)
Darya Stepanenko, Yuzhang Wang, Carlos L Simmerling
Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein. Viruses 16 (7) (2024)
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos L Simmerling, Ramón Alain Miranda-Quintana
k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations. Journal of chemical theory and computation (2024)
Darya Stepanenko, Stephanie Budhan, Carlos L Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. Journal of chemical information and modeling (2023)
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, Gerardo Andrés Cisneros, Vinícius Wilian D Cruzeiro, Negin Forouzesh, Timothy J Giese, Andreas W Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R Machado, Hai Minh Nguyen, Kurt A O'Hearn, Alexey V Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E Cheatham, Daniel R Roe, Adrian E Roitberg, Carlos L Simmerling, Darrin M York, Maria C Nagan, Kenneth M Merz
AmberTools. Journal of chemical information and modeling (2023)
Juan Alcantara, Kelley Chiu, John D Bickel, Robert C Rizzo, Carlos L Simmerling
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)
Darya Stepanenko, Stephanie Budhan, Carlos L Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. Journal of chemical information and modeling (2023)
Darya Stepanenko, Stephanie Budhan, Carlos L Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. Journal of chemical information and modeling (2023)
Koushik Kasavajhala, Carlos L Simmerling
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)
Ernest Glukhov, Dmytro Kalitin, Darya Stepanenko, Yimin Zhu, Thu Nguen, George Jones, Carlos L Simmerling, Julie C Mitchell, Sandor Vajda, Ken A Dill, Dzmitry Padhorny, Dima Kozakov
MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction. bioRxiv : the preprint server for biology (2023)
Darya Stepanenko, Stephanie Budhan, Carlos L Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. Journal of chemical information and modeling 63 (4) (2023)
Darya Stepanenko, Stephanie Budhan, Carlos L Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. Journal of chemical information and modeling 63 (4) (2023)
Mina Nikolić, Sandi Brudar, Evangelos Coutsias, Ken A Dill, Miha Lukšič, Carlos L Simmerling, Barbara Hribar-Lee
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International journal of molecular sciences 23 (23) (2022)
Kenneth Lam, Koushik Kasavajhala, Sarah Gunasekera, Carlos L Simmerling
Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir. Journal of chemical theory and computation 18 (6) (2022)
Mina Nikolić, Sandi Brudar, Evangelos Coutsias, Ken A Dill, Miha Lukšič, Carlos L Simmerling, Barbara Hribar-Lee
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International journal of molecular sciences 23 (23) (2022)
Mina Nikolić, Sandi Brudar, Evangelos Coutsias, Ken A Dill, Miha Lukšič, Carlos L Simmerling, Barbara Hribar-Lee
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International journal of molecular sciences 23 (23) (2022)
Mina Nikolić, Sandi Brudar, Evangelos Coutsias, Ken A Dill, Miha Lukšič, Carlos L Simmerling, Barbara Hribar-Lee
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International journal of molecular sciences 23 (23) (2022)
Mina Nikolić, Sandi Brudar, Evangelos Coutsias, Ken A Dill, Miha Lukšič, Carlos L Simmerling, Barbara Hribar-Lee
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International journal of molecular sciences 23 (23) (2022)
Junjie Zou, Shifeng Xiao, Carlos L Simmerling, Daniel P Raleigh
Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. The journal of physical chemistry. B 125 (13) (2021)
Lucy Fallon, Kellon A A Belfon, Lauren Raguette, Yuzhang Wang, Darya Stepanenko, Abbigayle Cuomo, Jose Guerra, Stephanie Budhan, Sarah Varghese, Christopher P Corbo, Robert C Rizzo, Carlos L Simmerling
Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket. Journal of the American Chemical Society 143 (30) (2021)
Emiliano Brini, Carlos L Simmerling, Ken A Dill
Protein storytelling through physics. Science (New York, N.Y.) 370 (6520) (2021)
Sang Hoon Kim, Fiona L Kearns, Mia A Rosenfeld, Lorenzo Casalino, Micah J Papanikolas, Carlos L Simmerling, Rommie Elizabeth Amaro, Ronit Freeman
GlycoGrip : Cell Surface-Inspired Universal Sensor for Betacoronaviruses. ACS central science 8 (1) (2021)
Junjie Zou, Zhipeng Li, Shuai Liu, Chunwang Peng, Dong Fang, Xiao Wan, Zhixiong Lin, Tai-Sung Lee, Daniel P Raleigh, Mingjun Yang, Carlos L Simmerling
Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. Journal of chemical theory and computation 17 (6) (2021)
James N Iuliano, Jinnette Tolentino Collado, Agnieszka A Gil, Pavithran T Ravindran, Andras Lukacs, SeungYoun Shin, Helena A Woroniecka, Katrin Adamczyk, James M Aramini, Uthama R Edupuganti, Christopher R Hall, Gregory M Greetham, Igor V Sazanovich, Ian P Clark, Taraneh Daryaee, Jared E Toettcher, Jarrod B French, Kevin H Gardner, Carlos L Simmerling, Stephen R Meech, Peter J Tonge
Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix. ACS chemical biology 15 (10) (2020)
Koushik Kasavajhala, Kenneth Lam, Carlos L Simmerling
Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations. Journal of chemical theory and computation 16 (12) (2020)
Junjie Zou, Carlos L Simmerling, Daniel P Raleigh
Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach. The journal of physical chemistry. B 123 (49) (2019)
Delaram Ghoreishi, David S Cerutti, Zachary Fallon, Carlos L Simmerling, Adrian E Roitberg
Fast Implementation of the Nudged Elastic Band Method in AMBER. Journal of chemical theory and computation 15 (8) (2019)
Junjie Zou, Chuan Tian, Carlos L Simmerling
Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. Journal of computer-aided molecular design 33 (12) (2019)
Chuan Tian, Koushik Kasavajhala, Kellon A A Belfon, Lauren Raguette, He Huang, Angela N Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos L Simmerling
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. Journal of chemical theory and computation 16 (1) (2019)
He Huang, Carlos L Simmerling
Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs. Journal of chemical theory and computation 14 (11) (2018)
Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos L Simmerling, Evangelos A Coutsias
Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. Journal of chemical information and modeling 57 (4) (2017)
Haoquan Li, Anton V Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman, Dmitry O Zharkov, Carlos L Simmerling
DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase. Journal of the American Chemical Society 139 (7) (2017)

Carlos L Simmerling.css-eqlu8i{font-size:small;padding-left:4px;} (Carlos Simmerling)

Publication Activity (10 Years)

Top Topics

Top Venues

Carlos L Simmerling (Carlos Simmerling)