CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules: CHARMM-GUI Ligand Reader and Modeler for CHARMM Force Field Generation of Small Molecules von Kim, Seonghoon, Lee, Jumin, Jo, Sunhwan, Brooks, Charles L., Lee, Hui Sun, Im, Wonpil

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Automated builder and database of protein/membrane complexes for molecular dynamics simulations von Jo, Sunhwan, Kim, Taehoon, Im, Wonpil

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CHARMM-GUI: A web-based graphical user interface for CHARMM von Jo, Sunhwan, Kim, Taehoon, Iyer, Vidyashankara G, Im, Wonpil

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field von Lee, Jumin, Cheng, Xi, Swails, Jason M, Yeom, Min Sun, Eastman, Peter K, Lemkul, Justin A, Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S, Case, David A, Brooks, Charles L, MacKerell, Alexander D, Klauda, Jeffery B, Im, Wonpil

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Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation von Goel, Himanshu, Hazel, Anthony, Ustach, Vincent D, Jo, Sunhwan, Yu, Wenbo, MacKerell, Alexander D

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Glycan fragment database: a database of PDB-based glycan 3D structures von Jo, Sunhwan, Im, Wonpil

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String Method for Protein–Protein Binding Free-Energy Calculations von Suh, Donghyuk, Jo, Sunhwan, Jiang, Wei, Chipot, Chris, Roux, Benoît

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CHARMM‐GUI 10 years for biomolecular modeling and simulation von Jo, Sunhwan, Cheng, Xi, Lee, Jumin, Kim, Seonghoon, Park, Sang‐Jun, Patel, Dhilon S., Beaven, Andrew H., Lee, Kyu Il, Rui, Huan, Park, Soohyung, Lee, Hui Sun, Roux, Benoît, MacKerell, Alexander D., Klauda, Jeffrey B., Qi, Yifei, Im, Wonpil

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Application of site-identification by ligand competitive saturation in computer-aided drug design von Goel, Himanshu, Hazel, Anthony, Yu, Wenbo, Jo, Sunhwan, MacKerell, Alexander D

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Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank von Park, Sang-Jun, Lee, Jumin, Patel, Dhilon S, Ma, Hongjing, Lee, Hui Sun, Jo, Sunhwan, Im, Wonpil

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Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization von Ustach, Vincent D, Lakkaraju, Sirish Kaushik, Jo, Sunhwan, Yu, Wenbo, Jiang, Wenjuan, MacKerell, Alexander D

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Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-H... von MacKerell, Alexander D., Jo, Sunhwan, Lakkaraju, Sirish Kaushik, Lind, Christoffer, Yu, Wenbo

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CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field von Kognole, Abhishek A., Lee, Jumin, Park, Sang‐Jun, Jo, Sunhwan, Chatterjee, Payal, Lemkul, Justin A., Huang, Jing, MacKerell, Alexander D., Im, Wonpil

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GPU‐specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations von Zhao, Mingtian, Kognole, Abhishek A., Jo, Sunhwan, Tao, Aoxiang, Hazel, Anthony, MacKerell, Alexander D.

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Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins von Jo, Sunhwan, Song, Kevin C., Desaire, Heather, MacKerell Jr, Alexander D., Im, Wonpil

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Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology von Yu, Wenbo, Jo, Sunhwan, Lakkaraju, Sirish Kaushik, Weber, David J., MacKerell, Alexander D.

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PBEQ-Solver for online visualization of electrostatic potential of biomolecules von Jo, Sunhwan, Vargyas, Miklos, Vasko-Szedlar, Judit, Roux, Benoît, Im, Wonpil

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Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics von Wu, Emilia L., Engström, Olof, Jo, Sunhwan, Stuhlsatz, Danielle, Yeom, Min Sun, Klauda, Jeffery B., Widmalm, Göran, Im, Wonpil

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Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model von Das, Avisek, Gur, Mert, Cheng, Mary Hongying, Jo, Sunhwan, Bahar, Ivet, Roux, Benoît

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CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues von Jo, Sunhwan, Cheng, Xi, Islam, Shahidul M, Huang, Lei, Rui, Huan, Zhu, Allen, Lee, Hui Sun, Qi, Yifei, Han, Wei, Vanommeslaeghe, Kenno, MacKerell, Jr, Alexander D, Roux, Benoît, Im, Wonpil

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