Carlos Simmerling

Affiliations

Department of Chemistry, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.

Publications (32)

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

The Journal of biological chemistry

Avec: Elliot J Crooks , Brandon A Irizarry , Martine Ziliox , Toru Kawakami , Tiffany Victor , Feng Xu , Hironobu Hojo , Kelley Chiu , Carlos Simmerling , William E Van Nostrand , Steven O Smith , Lisa M Miller

Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.

Journal of chemical theory and computation

Avec: Koushik Kasavajhala , Kenneth Lam , Carlos Simmerling

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

ArXiv

Avec: Xin Cao , Michelle H Hummel , Yuzhang Wang , Carlos Simmerling , Evangelos A Coutsias

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

Avec: Lauren E Raguette , Sarah S Gunasekera , Rebeca I Diaz Ventura , Ethan Aminov , Jason T Linzer , Diksha Parwana , Qin Wu , Carlos Simmerling , Maria C Nagan

Protein storytelling through physics.

Science (New York, N.Y.)

Avec: Emiliano Brini , Carlos Simmerling , Ken Dill

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

Avec: 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 Simmerling

Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein.

Viruses

Avec: Darya Stepanenko , Yuzhang Wang , Carlos Simmerling

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

Journal of chemical theory and computation

Avec: Lexin Chen , Daniel R Roe , Matthew Kochert , Carlos Simmerling , Ramón Alain Miranda-Quintana

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

Avec: Koushik Kasavajhala , Carlos Simmerling

AmberTools.

Journal of chemical information and modeling

Avec: David A Case , Hasan Metin Aktulga , Kellon Belfon , David S Cerutti , G 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 , Matias 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 Roitberg , Carlos Simmerling , Darrin M York , Maria C Nagan , Kenneth M Merz

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

bioRxiv : the preprint server for biology

Avec: Ernest Glukhov , Dmytro Kalitin , Darya Stepanenko , Yimin Zhu , Thu Nguen , George Jones , Carlos Simmerling , Julie C Mitchell , Sandor Vajda , Ken A Dill , Dzmitry Padhorny , Dima Kozakov

Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach.

The journal of physical chemistry. B

Avec: Junjie Zou , Carlos 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

Avec: Junjie Zou , Shifeng Xiao , Carlos Simmerling , Daniel P Raleigh

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

bioRxiv : the preprint server for biology

Avec: Lorenzo Casalino , Abigail Dommer , Zied Gaieb , Emilia P Barros , Terra Sztain , Surl-Hee Ahn , Anda Trifan , Alexander Brace , Anthony Bogetti , Heng Ma , Hyungro Lee , Matteo Turilli , Syma Khalid , Lillian Chong , Carlos Simmerling , David J Hardy , Julio D C Maia , James C Phillips , Thorsten Kurth , Abraham Stern , Lei Huang , John McCalpin , Mahidhar Tatineni , Tom Gibbs , John E Stone , Shantenu Jha , Arvind Ramanathan , Rommie E Amaro

ACS central science

Avec: Sang Hoon Kim , Fiona L Kearns , Mia A Rosenfeld , Lorenzo Casalino , Micah J Papanikolas , Carlos Simmerling , Rommie E Amaro , Ronit Freeman

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

Journal of chemical theory and computation

Avec: Xin Cao , Michelle H Hummel , Yuzhang Wang , Carlos Simmerling , Evangelos A Coutsias

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.

The international journal of high performance computing applications

Avec: Lorenzo Casalino , Abigail C Dommer , Zied Gaieb , Emilia P Barros , Terra Sztain , Surl-Hee Ahn , Anda Trifan , Alexander Brace , Anthony T Bogetti , Austin Clyde , Heng Ma , Hyungro Lee , Matteo Turilli , Syma Khalid , Lillian T Chong , Carlos Simmerling , David J Hardy , Julio Dc Maia , James C Phillips , Thorsten Kurth , Abraham C Stern , Lei Huang , John D McCalpin , Mahidhar Tatineni , Tom Gibbs , John E Stone , Shantenu Jha , Arvind Ramanathan , Rommie E Amaro

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

Biophysical journal

Avec: Ernest Glukhov , Dmytro Kalitin , Darya Stepanenko , Yimin Zhu , Thu Nguyen , George Jones , Taras Patsahan , Carlos Simmerling , Julie C Mitchell , Sandor Vajda , Ken A Dill , Dzmitry Padhorny , Dima Kozakov

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

bioRxiv : the preprint server for biology

Avec: E P Barros , L Casalino , Z Gaieb , A C Dommer , Y Wang , L Fallon , L Raguette , K Belfon , C Simmerling , R E Amaro

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

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

SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein.

Journal of chemical information and modeling

Avec: Darya Stepanenko , Stephanie Budhan , Carlos Simmerling

SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines.

Science immunology

Avec: John E Bowen , Young-Jun Park , Cameron Stewart , Jack T Brown , William K Sharkey , Alexandra C Walls , Anshu Joshi , Kaitlin R Sprouse , Matthew McCallum , M Alejandra Tortorici , Nicholas M Franko , Jennifer K Logue , Ignacio G Mazzitelli , Annalee W Nguyen , Rui P Silva , Yimin Huang , Jun Siong Low , Josipa Jerak , Sasha W Tiles , Kumail Ahmed , Asefa Shariq , Jennifer M Dan , Zeli Zhang , Daniela Weiskopf , Alessandro Sette , Gyorgy Snell , Christine M Posavad , Najeeha Talat Iqbal , Jorge Geffner , Alessandra Bandera , Andrea Gori , Federica Sallusto , Jennifer A Maynard , Shane Crotty , Wesley C Van Voorhis , Carlos Simmerling , Renata Grifantini , Helen Y Chu , Davide Corti , David Veesler

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.

Journal of chemical information and modeling

Avec: 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 P 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 Simmerling , Maria C Nagan

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids.

Journal of chemical theory and computation

Avec: Lauren E Raguette , Abbigayle E Cuomo , Kellon A A Belfon , Chuan Tian , Victoria Hazoglou , Gabriela Witek , Stephen M Telehany , Qin Wu , Carlos Simmerling

Fast Implementation of the Nudged Elastic Band Method in AMBER.

Journal of chemical theory and computation

Avec: Delaram Ghoreishi , David S Cerutti , Zachary Fallon , Carlos Simmerling , Adrian E Roitberg

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.

Journal of chemical theory and computation

Avec: Chuan Tian , Koushik Kasavajhala , Kellon A A Belfon , Lauren Raguette , He Huang , Angela N Migues , John Bickel , Yuzhang Wang , Jorge Pincay , Qin Wu , Carlos 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

Avec: Junjie Zou , Chuan Tian , Carlos Simmerling

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

Biophysical journal

Avec: Emilia P Barros , Lorenzo Casalino , Zied Gaieb , Abigail C Dommer , Yuzhang Wang , Lucy Fallon , Lauren Raguette , Kellon Belfon , Carlos Simmerling , Rommie E Amaro

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

Journal of chemical theory and computation

Avec: Kenneth Lam , Koushik Kasavajhala , Sarah Gunasekera , Carlos Simmerling

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

Protein science : a publication of the Protein Society

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

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions.

International journal of molecular sciences

Avec: Mina Nikolić , Sandi Brudar , Evangelos Coutsias , Ken A Dill , Miha Lukšič , Carlos Simmerling , Barbara Hribar-Lee

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

bioRxiv : the preprint server for biology

Avec: Lexin Chen , Daniel R Roe , Matthew Kochert , Carlos Simmerling , Ramón Alain Miranda-Quintana

Réseau de co-auteurs

Yuzhang Wang 6 collaborations

Koushik Kasavajhala 5 collaborations

Darya Stepanenko 5 collaborations

Lorenzo Casalino 4 collaborations

Rommie E Amaro 4 collaborations

Qin Wu 3 collaborations

Maria C Nagan 3 collaborations

Kellon A A Belfon 3 collaborations

Lauren Raguette 3 collaborations

Daniel R Roe 3 collaborations

Ken A Dill 3 collaborations

Junjie Zou 3 collaborations

Daniel P Raleigh 3 collaborations

Zied Gaieb 3 collaborations

Emilia P Barros 3 collaborations

Chuan Tian 3 collaborations

Kelley Chiu 2 collaborations

Kenneth Lam 2 collaborations

Xin Cao 2 collaborations

Michelle H Hummel 2 collaborations

Evangelos A Coutsias 2 collaborations

Lauren E Raguette 2 collaborations

Rebeca I Diaz Ventura 2 collaborations

Ethan Aminov 2 collaborations

Jason T Linzer 2 collaborations

Lucy Fallon 2 collaborations

Stephanie Budhan 2 collaborations

Robert C Rizzo 2 collaborations

Lexin Chen 2 collaborations

Matthew Kochert 2 collaborations

Ramón Alain Miranda-Quintana 2 collaborations

Kellon Belfon 2 collaborations

David S Cerutti 2 collaborations

Ernest Glukhov 2 collaborations

Dmytro Kalitin 2 collaborations

Yimin Zhu 2 collaborations

George Jones 2 collaborations

Julie C Mitchell 2 collaborations

Sandor Vajda 2 collaborations

Dzmitry Padhorny 2 collaborations

Dima Kozakov 2 collaborations

Terra Sztain 2 collaborations

Surl-Hee Ahn 2 collaborations

Anda Trifan 2 collaborations

Alexander Brace 2 collaborations

Heng Ma 2 collaborations

Hyungro Lee 2 collaborations

Matteo Turilli 2 collaborations

Syma Khalid 2 collaborations

David J Hardy 2 collaborations

James C Phillips 2 collaborations

Thorsten Kurth 2 collaborations

Lei Huang 2 collaborations

Mahidhar Tatineni 2 collaborations

Tom Gibbs 2 collaborations

John E Stone 2 collaborations

Shantenu Jha 2 collaborations

Arvind Ramanathan 2 collaborations

Abigail C Dommer 2 collaborations

Elliot J Crooks 1 collaboration

Brandon A Irizarry 1 collaboration

Martine Ziliox 1 collaboration

Toru Kawakami 1 collaboration

Tiffany Victor 1 collaboration

Feng Xu 1 collaboration

Hironobu Hojo 1 collaboration

William E Van Nostrand 1 collaboration

Steven O Smith 1 collaboration

Lisa M Miller 1 collaboration

Sarah S Gunasekera 1 collaboration

Diksha Parwana 1 collaboration

Emiliano Brini 1 collaboration

Ken Dill 1 collaboration

Abbigayle Cuomo 1 collaboration

Jose Guerra 1 collaboration

Sarah Varghese 1 collaboration

Christopher P Corbo 1 collaboration

David A Case 1 collaboration

Hasan Metin Aktulga 1 collaboration

G Andrés Cisneros 1 collaboration

Vinícius Wilian D Cruzeiro 1 collaboration

Negin Forouzesh 1 collaboration

Timothy J Giese 1 collaboration

Andreas W Götz 1 collaboration

Holger Gohlke 1 collaboration

Saeed Izadi 1 collaboration

Mehmet C Kaymak 1 collaboration

Edward King 1 collaboration

Tom Kurtzman 1 collaboration

Tai-Sung Lee 1 collaboration

Pengfei Li 1 collaboration

Jian Liu 1 collaboration

Tyler Luchko 1 collaboration

Ray Luo 1 collaboration

Madushanka Manathunga 1 collaboration

Matias R Machado 1 collaboration

Hai Minh Nguyen 1 collaboration

Kurt A O'Hearn 1 collaboration

Alexey V Onufriev 1 collaboration

Feng Pan 1 collaboration

Sergio Pantano 1 collaboration

Ruxi Qi 1 collaboration

Ali Rahnamoun 1 collaboration

Ali Risheh 1 collaboration

Stephan Schott-Verdugo 1 collaboration

Akhil Shajan 1 collaboration

Jason Swails 1 collaboration

Junmei Wang 1 collaboration

Haixin Wei 1 collaboration

Xiongwu Wu 1 collaboration

Yongxian Wu 1 collaboration

Shi Zhang 1 collaboration

Shiji Zhao 1 collaboration

Qiang Zhu 1 collaboration

Thomas E Cheatham 1 collaboration

Adrian Roitberg 1 collaboration

Darrin M York 1 collaboration

Kenneth M Merz 1 collaboration

Thu Nguen 1 collaboration

Shifeng Xiao 1 collaboration

Abigail Dommer 1 collaboration

Anthony Bogetti 1 collaboration

Lillian Chong 1 collaboration

Julio D C Maia 1 collaboration

Abraham Stern 1 collaboration

John McCalpin 1 collaboration

Sang Hoon Kim 1 collaboration

Fiona L Kearns 1 collaboration

Mia A Rosenfeld 1 collaboration

Micah J Papanikolas 1 collaboration

Ronit Freeman 1 collaboration

Anthony T Bogetti 1 collaboration

Austin Clyde 1 collaboration

Lillian T Chong 1 collaboration

Julio Dc Maia 1 collaboration

Abraham C Stern 1 collaboration

John D McCalpin 1 collaboration

Thu Nguyen 1 collaboration

Taras Patsahan 1 collaboration

E P Barros 1 collaboration

L Casalino 1 collaboration

Z Gaieb 1 collaboration

A C Dommer 1 collaboration

Y Wang 1 collaboration

L Fallon 1 collaboration

L Raguette 1 collaboration

K Belfon 1 collaboration

C Simmerling 1 collaboration

R E Amaro 1 collaboration

Juan Alcantara 1 collaboration

John D Bickel 1 collaboration

John E Bowen 1 collaboration

Young-Jun Park 1 collaboration

Cameron Stewart 1 collaboration

Jack T Brown 1 collaboration

William K Sharkey 1 collaboration

Alexandra C Walls 1 collaboration

Anshu Joshi 1 collaboration

Kaitlin R Sprouse 1 collaboration

Matthew McCallum 1 collaboration

M Alejandra Tortorici 1 collaboration

Nicholas M Franko 1 collaboration

Jennifer K Logue 1 collaboration

Ignacio G Mazzitelli 1 collaboration

Annalee W Nguyen 1 collaboration

Rui P Silva 1 collaboration

Yimin Huang 1 collaboration

Jun Siong Low 1 collaboration

Josipa Jerak 1 collaboration

Sasha W Tiles 1 collaboration

Kumail Ahmed 1 collaboration

Asefa Shariq 1 collaboration

Jennifer M Dan 1 collaboration

Zeli Zhang 1 collaboration

Daniela Weiskopf 1 collaboration

Alessandro Sette 1 collaboration

Gyorgy Snell 1 collaboration

Christine M Posavad 1 collaboration

Najeeha Talat Iqbal 1 collaboration

Jorge Geffner 1 collaboration

Alessandra Bandera 1 collaboration

Andrea Gori 1 collaboration

Federica Sallusto 1 collaboration

Jennifer A Maynard 1 collaboration

Shane Crotty 1 collaboration

Wesley C Van Voorhis 1 collaboration

Renata Grifantini 1 collaboration

Helen Y Chu 1 collaboration

Davide Corti 1 collaboration

David Veesler 1 collaboration

Aalim S Abdullah 1 collaboration

Colleen E Kirkup 1 collaboration

Vinay R Bijoor 1 collaboration

Jiyun Jung 1 collaboration

Sophie Huang 1 collaboration

Chi Gee Tse 1 collaboration

Emily Álvarez Toucet 1 collaboration

Hugo P Onghai 1 collaboration

Arghya P Ghosh 1 collaboration

Alex C Grodzki 1 collaboration

Emilee R Haines 1 collaboration

Aditya S Iyer 1 collaboration

Mark K Khalil 1 collaboration

Alexander P Leong 1 collaboration

Michael A Neuhaus 1 collaboration

Joseph Park 1 collaboration

Asir Shahid 1 collaboration

Matthew Xie 1 collaboration

Jan M Ziembicki 1 collaboration

Abbigayle E Cuomo 1 collaboration

Victoria Hazoglou 1 collaboration

Gabriela Witek 1 collaboration

Stephen M Telehany 1 collaboration

Delaram Ghoreishi 1 collaboration

Zachary Fallon 1 collaboration

Adrian E Roitberg 1 collaboration

He Huang 1 collaboration

Angela N Migues 1 collaboration

John Bickel 1 collaboration

Jorge Pincay 1 collaboration

Sarah Gunasekera 1 collaboration

Lakshan Manathunga 1 collaboration

Rehana Akter 1 collaboration

Alexander Zhyvoloup 1 collaboration

Mina Nikolić 1 collaboration

Sandi Brudar 1 collaboration

Evangelos Coutsias 1 collaboration

Miha Lukšič 1 collaboration

Barbara Hribar-Lee 1 collaboration