Search results for "CHARMM"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
100	Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli	Implementation and Characterization of Protein Folding on a Desktop Computational Grid - Is CHARMM a Suitable Candidate for the United Devices MetaProcessor?	IPDPS	2003	DBLP DOI BibTeX RDF	widely distributed computing, CHARMM, United Devices MetaProcessor, workload characterization, protein folding, search algorithms, desktop grids
91	Michela Taufer, Egon Perathoner, Andrea Cavalli, Amedeo Caflisch, Thomas Stricker	Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?.	IPDPS	2002	DBLP DOI BibTeX RDF	cluster of PCs, distributed molecular dynamics, middleware, distributed computation, message passing, performance optimization, performance tuning
78	Siegfried Benkner, Christian Schröder, Mária Lucká, Othmar Steinhauser	Grid Services for Parallel Molecular Dynamics with NAMD and CHARMM.	ICCSA (1)	2008	DBLP DOI BibTeX RDF	NAMD, CHARMM, ionic liquid, Grid service, molecular dynamics
53	Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli, Amedeo Caflisch	Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform.	CCGRID	2003	DBLP DOI BibTeX RDF	data and task parallelism, CHARMM, United Devices MetaProcessor, computational grid, Protein folding, best-first search
49	Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks III, Hui Sun Lee, Wonpil Im	CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.	J. Comput. Chem.	2017	DBLP DOI BibTeX RDF
49	Kenno Vanommeslaeghe, Elizabeth Hatcher, Chayan Acharya, Sibsankar Kundu, Shijun Zhong, Jihyun Shim, Eva Darian, Olgun Guvench, Pedro E. M. Lopes, Igor Vorobyov, Alexander D. MacKerell Jr.	CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
49	Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im	CHARMM-GUI: A web-based graphical user interface for CHARMM.	J. Comput. Chem.	2008	DBLP DOI BibTeX RDF
47	Anand Natrajan, Anthony D. Fox, Marty A. Humphrey, Andrew S. Grimshaw, Nancy Wilkins-Diehr, Michael F. Crowley, Charles L. Brooks III	Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion.	HPDC	2001	DBLP DOI BibTeX RDF
44	Bruce Lowekamp, Adam Beguelin	ECO: Efficient Collective Operations for Communication on Heterogeneous Networks.	IPPS	1996	DBLP DOI BibTeX RDF
25	Zakaria Bouchouireb, Steeve H. Thany, Jean-Yves Le Questel	Development of CHARMM compatible force field parameters and molecular dynamics simulations for the pesticide flupyradifurone.	J. Comput. Chem.	2024	DBLP DOI BibTeX RDF
25	Rojalin Pradhan, Sibarama Panigrahi, Prabhat K. Sahu	Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
25	Hugo Guterres, Wonpil Im	CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
25	András F. Wacha, Justin A. Lemkul	charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
25	Sai Lakshmana Vankayala, Luke C. Warrensford, Amanda R. Pittman, Benjamin C. Pollard, Fiona L. Kearns, Joseph D. Larkin, H. Lee Woodcock III	CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
25	Andrada-Elena Terteci-Popescu, Titus Adrian Beu	Branched polyethyleneimine: CHARMM force field and molecular dynamics simulations.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
25	Abhishek A. Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang 0004, Alexander D. MacKerell Jr., Wonpil Im	CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
25	Thomas Giannos, Samo Lesnik, Urban Bren, Milan Hodoscek, Tatiana Domratcheva, Ana-Nicoleta Bondar	CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Hugo Guterres, Sang-Jun Park, Han Zhang 0028, Wonpil Im	CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Ya Gao 0004, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, Yifei Qi, Jeffery B. Klauda, Göran Widmalm, Syma Khalid, Wonpil Im	CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Soohyung Park, Yeol Kyo Choi, Seonghoon Kim, Jumin Lee, Wonpil Im	CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Hugo Guterres, Sang-Jun Park, Yiwei Cao, Wonpil Im	CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Han Zhang 0028, Seonghoon Kim, Timothy J. Giese, Tai-Sung Lee, Jumin Lee, Darrin M. York, Wonpil Im	CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Anmol Kumar, Ozge Yoluk, Alexander D. MacKerell Jr.	FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.	J. Comput. Chem.	2020	DBLP DOI BibTeX RDF
25	Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam, Benoît Roux, Wonpil Im	CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations.	J. Comput. Chem.	2020	DBLP DOI BibTeX RDF
25	Ida Friis, Alexey Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov	Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field.	J. Comput. Chem.	2020	DBLP DOI BibTeX RDF
25	Shujie Fan, Bogdan I. Iorga, Oliver Beckstein	Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.	J. Comput. Aided Mol. Des.	2020	DBLP DOI BibTeX RDF
25	Travis Hesketh	pygen-structures: A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield.	J. Open Source Softw.	2020	DBLP DOI BibTeX RDF
25	Yifei Qi, Jumin Lee, Jeffery B. Klauda, Wonpil Im	CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems.	J. Comput. Chem.	2019	DBLP DOI BibTeX RDF
25	Fang-Yu Lin, Alexander D. MacKerell Jr.	Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields.	J. Chem. Inf. Model.	2019	DBLP DOI BibTeX RDF
25	Suliman Adam, Michaela Knapp-Mohammady, Jun Yi, Ana-Nicoleta Bondar	Revised CHARMM force field parameters for iron-containing cofactors of photosystem II.	J. Comput. Chem.	2018	DBLP DOI BibTeX RDF
25	Titus Adrian Beu, Andrada-Elena Ailenei, Alexandra Farcas	CHARMM force field for protonated polyethyleneimine.	J. Comput. Chem.	2018	DBLP DOI BibTeX RDF
25	Titus Adrian Beu, Alexandra Farcas	CHARMM force field and molecular dynamics simulations of protonated polyethylenimine.	J. Comput. Chem.	2017	DBLP DOI BibTeX RDF
25	Pin-Chia Hsu, Bart M. H. Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S. Patel, Siewert J. Marrink, Yifei Qi, Syma Khalid, Wonpil Im	CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.	J. Comput. Chem.	2017	DBLP DOI BibTeX RDF
25	Sunhwan Jo, Xi Cheng, Jumin Lee, Seonghoon Kim, Sang-Jun Park, Dhilon S. Patel, Andrew H. Beaven, Kyu Il Lee, Huan Rui, Soohyung Park, Hui Sun Lee, Benoît Roux, Alexander D. MacKerell Jr., Jeffrey B. Klauda, Yifei Qi, Wonpil Im	CHARMM-GUI 10 years for biomolecular modeling and simulation.	J. Comput. Chem.	2017	DBLP DOI BibTeX RDF
25	Jessica K. Gagnon, Sean M. Law, Charles L. Brooks III	Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.	J. Comput. Chem.	2016	DBLP DOI BibTeX RDF
25	You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. MacKerell Jr., Lennart Nilsson	Additive CHARMM force field for naturally occurring modified ribonucleotides.	J. Comput. Chem.	2016	DBLP DOI BibTeX RDF
25	Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer	TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.	J. Chem. Inf. Model.	2016	DBLP DOI BibTeX RDF
25	Micholas Dean Smith, J. Srinivasa Rao, Elizabeth Segelken, Luis Cruz 0003	Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields.	J. Chem. Inf. Model.	2015	DBLP DOI BibTeX RDF
25	Antti-Pekka Hynninen, Michael F. Crowley	New faster CHARMM molecular dynamics engine.	J. Comput. Chem.	2014	DBLP DOI BibTeX RDF
25	Dina T. Mirijanian, Ranjan V. Mannige, Ronald N. Zuckermann, Stephen Whitelam	Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.	J. Comput. Chem.	2014	DBLP DOI BibTeX RDF
25	Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M. Venable, Jeffery B. Klauda, Wonpil Im	CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.	J. Comput. Chem.	2014	DBLP DOI BibTeX RDF
25	Saleh Riahi, Christopher N. Rowley	The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.	J. Comput. Chem.	2014	DBLP DOI BibTeX RDF
25	Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, Wonpil Im	CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations.	J. Chem. Inf. Model.	2014	DBLP DOI BibTeX RDF
25	Jennifer L. Knight, Joseph D. Yesselman, Charles L. Brooks III	Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.	J. Comput. Chem.	2013	DBLP DOI BibTeX RDF
25	Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im	CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
25	Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda, Wonpil Im	CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
25	Edyta Malolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard N. Fejer, Joanne M. Carr, David J. Wales	Erratum: Symmetrization of the AMBER and CHARMM force fields [J. Comp. Chem. 31, 1402].	J. Comput. Chem.	2012	DBLP DOI BibTeX RDF
25	Wenbo Yu 0002, Xibing He, Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.	Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations.	J. Comput. Chem.	2012	DBLP DOI BibTeX RDF
25	Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.	Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing.	J. Chem. Inf. Model.	2012	DBLP DOI BibTeX RDF
25	Kenno Vanommeslaeghe, E. Prabhu Raman, Alexander D. MacKerell Jr.	Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges.	J. Chem. Inf. Model.	2012	DBLP DOI BibTeX RDF
25	Aurélien Grosdidier, Vincent Zoete, Olivier Michielin	Fast docking using the CHARMM force field with EADock DSS.	J. Comput. Chem.	2011	DBLP DOI BibTeX RDF
25	Elizabeth J. Denning, U. Deva Priyakumar, Lennart Nilsson, Alexander D. MacKerell Jr.	Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA.	J. Comput. Chem.	2011	DBLP DOI BibTeX RDF
25	Narayan Ganesan, Michela Taufer, Brad A. Bauer, Sandeep Patel	FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME.	IPDPS Workshops	2011	DBLP DOI BibTeX RDF
25	Edyta Malolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard N. Fejer, David J. Wales	Symmetrization of the AMBER and CHARMM force fields.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
25	Bogdan Lev, Rui Zhang, Aurélien de la Lande, Dennis R. Salahub, Sergei Yu Noskov	The QM-MM interface for CHARMM-deMon.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
25	Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus	CHARMM: The biomolecular simulation program.	J. Comput. Chem.	2009	DBLP DOI BibTeX RDF
25	Bharat Sukhwani, Martin C. Herbordt	FPGA-based acceleration of CHARMM-potential minimization.	HPRCTA@SC	2009	DBLP DOI BibTeX RDF
25	Carl-Johan Högberg, Alexei M. Nikitin, Alexander Lyubartsev	Modification of the CHARMM force field for DMPC lipid bilayer.	J. Comput. Chem.	2008	DBLP DOI BibTeX RDF
25	Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III	CHARMMing: A New, Flexible Web Portal for CHARMM.	J. Chem. Inf. Model.	2008	DBLP DOI BibTeX RDF
25	Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr., Darrin M. York	CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.	J. Comput. Chem.	2007	DBLP DOI BibTeX RDF
25	H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks	Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations.	J. Comput. Chem.	2007	DBLP DOI BibTeX RDF
25	Jie Hu, Ao Ma, Aaron R. Dinner	Monte Carlo simulations of biomolecules: The MC module in CHARMM.	J. Comput. Chem.	2006	DBLP DOI BibTeX RDF
25	Alba T. Macias, Alexander D. MacKerell Jr.	CH/ interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field.	J. Comput. Chem.	2005	DBLP DOI BibTeX RDF
25	Anand Natrajan, Michael F. Crowley, Nancy Wilkins-Diehr, Marty A. Humphrey, Anthony D. Fox, Andrew S. Grimshaw, Charles L. Brooks III	Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion.	Concurr. Comput. Pract. Exp.	2004	DBLP DOI BibTeX RDF
25	Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III	CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.	J. Comput. Chem.	2004	DBLP DOI BibTeX RDF
25	Sandeep Patel, Charles L. Brooks III	CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.	J. Comput. Chem.	2004	DBLP DOI BibTeX RDF
25	Guosheng Wu, Daniel H. Robertson, Charles L. Brooks III, Michal Vieth	Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm.	J. Comput. Chem.	2003	DBLP DOI BibTeX RDF
25	Markus J. Loferer, Hannes H. Loeffler, Klaus R. Liedl	A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems.	J. Comput. Chem.	2003	DBLP DOI BibTeX RDF
25	Pavel Hobza, Martin Kabelác, Jirí Sponer, Petr Mejzlík, Jirí Vondrásek	Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results.	J. Comput. Chem.	1997	DBLP DOI BibTeX RDF
25	Marc C. Nicklaus	Conformational energies calculated by the molecular mechanics program CHARMm.	J. Comput. Chem.	1997	DBLP DOI BibTeX RDF
25	Cornelis J. M. Huige, Cornelis Altona	Force Field Parameters for Sulfates and Sulfamates Based on Ab Initio Calculations: Extensions of AMBER and CHARMm Fields.	J. Comput. Chem.	1995	DBLP DOI BibTeX RDF
25	Philippe Derreumaux, Guihua Zhang, Tamar Schlick, Bernard R. Brooks	A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications.	J. Comput. Chem.	1994	DBLP DOI BibTeX RDF
22	Guillermo A. Lopez, Michela Taufer, Patricia J. Teller	Evaluation of IEEE 754 floating-point arithmetic compliance across a wide range of heterogeneous computers.	Richard Tapia Celebration of Diversity in Computing Conference	2007	DBLP DOI BibTeX RDF	result divergences, scientific computation, heterogeneous computing
22	Youngjin Choi, Sung-Ryul Kim, Suntae Hwang, Karpjoo Jeong	A Grid Computing-Based Monte Carlo Docking Simulations Approach for Computational Chiral Discrimination.	RSFDGrC (2)	2005	DBLP DOI BibTeX RDF
22	Atul Dubey, Gaurav Sharma 0003, Constantinos Mavroidis, Silvina-Maria Tomassone, K. Nikitczuk, Martin L. Yarmush	Dynamics and Kinematics of Viral Protein Linear Nano-actuators for Bio-nano Robotic Systems.	ICRA	2004	DBLP DOI BibTeX RDF
22	Irina Chihaia, Thomas R. Gross	Effectiveness of simple memory models for performance prediction.	ISPASS	2004	DBLP DOI BibTeX RDF
22	Shamik D. Sharma, Ravi Ponnusamy, Bongki Moon, Yuan-Shin Hwang, Raja Das, Joel H. Saltz	Run-time and compile-time support for adaptive irregular problems.	SC	1994	DBLP DOI BibTeX RDF