Wonpil Im
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Computer Science
Wonpil Im's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
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Why Is Wonpil Im Influential?
(Suggest an Edit or Addition)According to Wikipedia, Wonpil Im is professor of Biological Sciences and Bioengineering at the Lehigh University and has been named the Presidential Endowed Chair in Health Science and Engineering. He has previously taught at University of Kansas. Wonpil Im has been appointed to KIAS scholar in 2016. Wonpil Im was a recipient of the 2017 Friedrich Wilhelm Bessel Research Award in Bioinformatics and Theoretical Biology, awarded by the Alexander von Humboldt Foundation.
Wonpil Im's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- CHARMM: The biomolecular simulation program (2009) (6525)
- CHARMM‐GUI: A web‐based graphical user interface for CHARMM (2008) (4069)
- CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field (2015) (1867)
- CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations (2014) (1410)
- CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. (2009) (1144)
- Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations (2007) (808)
- Generalized born model with a simple smoothing function (2003) (601)
- Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures (2004) (500)
- Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation (1998) (492)
- An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. (2003) (353)
- Theoretical and computational models of biological ion channels (2004) (351)
- Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. (2002) (343)
- Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. (2006) (302)
- CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. (2018) (256)
- CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field. (2015) (253)
- Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. (2002) (222)
- PBEQ-Solver for online visualization of electrostatic potential of biomolecules (2008) (222)
- CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules (2017) (214)
- A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. (2000) (201)
- Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. (2004) (190)
- Generalized solvent boundary potential for computer simulations (1999) (180)
- Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study (2015) (172)
- Ion channels, permeation, and electrostatics: insight into the function of KcsA. (2000) (163)
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates (2019) (153)
- CHARMM‐GUI 10 years for biomolecular modeling and simulation (2017) (150)
- Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. (2005) (148)
- Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. (2013) (147)
- Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins (2011) (145)
- Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane (2020) (142)
- CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. (2014) (135)
- Improving the CHARMM force field for polyunsaturated fatty acid chains. (2012) (135)
- Implicit solvation based on generalized Born theory in different dielectric environments. (2004) (133)
- E. coli outer membrane and interactions with OmpLA. (2014) (112)
- Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions. (2011) (112)
- Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane (2020) (111)
- Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. (2010) (109)
- CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides (2017) (106)
- Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations (2020) (105)
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. (2016) (104)
- Optimized atomic radii for protein continuum electrostatics solvation forces. (1999) (100)
- Cholesterol flip-flop: insights from free energy simulation studies. (2010) (100)
- CHARMM-GUI supports the Amber force fields. (2020) (94)
- Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. (2002) (90)
- Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. (2012) (85)
- A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties. (2014) (81)
- CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems (2013) (77)
- Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages (2011) (75)
- Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. (2016) (75)
- Molecular dynamics studies of ion permeation in VDAC. (2011) (72)
- CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. (2015) (72)
- Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. (2007) (72)
- CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application (2013) (71)
- Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank (2017) (70)
- Application of torsion angle molecular dynamics for efficient sampling of protein conformations (2005) (68)
- Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH. (2007) (66)
- Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. (2005) (64)
- Generation and application of new rat monoclonal antibodies against synthetic FLAG and OLLAS tags for improved immunodetection. (2008) (61)
- Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry (2001) (60)
- Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. (2016) (59)
- L-Met Activates Arabidopsis GLR Ca2+ Channels Upstream of ROS Production and Regulates Stomatal Movement. (2016) (59)
- Transmembrane helix tilting: insights from calculating the potential of mean force. (2008) (58)
- Refinement of NMR structures using implicit solvent and advanced sampling techniques. (2004) (57)
- Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa. (2010) (56)
- BamA POTRA Domain Interacts with a Native Lipid Membrane Surface. (2016) (55)
- De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. (2004) (55)
- Brownian dynamics simulations of ion transport through the VDAC. (2011) (51)
- Transmembrane helix assembly by window exchange umbrella sampling. (2012) (51)
- Potential pharmacological chaperones targeting cancer-associated MCL-1 and Parkinson disease-associated α-synuclein (2014) (48)
- How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? (2015) (48)
- Challenges in structural approaches to cell modeling. (2016) (47)
- CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. (2020) (45)
- Glycan fragment database: a database of PDB-based glycan 3D structures (2012) (44)
- Refinement of OprH-LPS Interactions by Molecular Simulations. (2017) (44)
- Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies. (2011) (43)
- An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. (2016) (43)
- Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores (2012) (43)
- Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors (2012) (42)
- Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics. (2016) (41)
- CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations (2014) (40)
- Lipopolysaccharide membrane building and simulation. (2015) (39)
- Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern (2021) (39)
- Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane (2021) (39)
- Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly. (2013) (37)
- Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction (2021) (37)
- CHARMM‐GUI Nanodisc Builder for modeling and simulation of various nanodisc systems (2019) (36)
- The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport. (2016) (36)
- Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling (2005) (36)
- Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature. (2016) (36)
- Modeling and simulation of bacterial outer membranes and interactions with membrane proteins. (2017) (35)
- CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers. (2021) (34)
- Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction (2020) (33)
- Multidimensional umbrella sampling and replica‐exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers (2014) (32)
- Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. (2017) (32)
- Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association. (2008) (32)
- Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. (2015) (32)
- Probing the U-shaped conformation of caveolin-1 in a bilayer. (2014) (31)
- Biophysical and functional characterization of Norrin signaling through Frizzled4 (2018) (31)
- Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending (2019) (31)
- A conserved αβ transmembrane interface forms the core of a compact T-cell receptor–CD3 structure within the membrane (2016) (31)
- Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern (2021) (31)
- Electrostatic free energy calculations using the generalized solvent boundary potential method (2002) (31)
- CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides (2021) (31)
- Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. (2014) (30)
- Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age. (2020) (30)
- Protein–protein interactions in actin–myosin binding and structural effects of R405Q mutation: A molecular dynamics study (2006) (30)
- Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations. (2011) (30)
- Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling (2013) (29)
- Transmembrane features governing Fc receptor CD16A assembly with CD16A signaling adaptor molecules (2017) (29)
- Application of solid-state NMR restraint potentials in membrane protein modeling. (2008) (29)
- Implementation and application of helix–helix distance and crossing angle restraint potentials (2007) (28)
- Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. (2011) (27)
- G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design (2016) (26)
- Unfolding of a ClC chloride transporter retains memory of its evolutionary history (2018) (26)
- Restraint potential and free energy decomposition formalism for helical tilting (2007) (25)
- NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes. (2012) (25)
- Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design (2012) (25)
- Protein dynamics and ion traffic in bacterioferritin. (2012) (24)
- CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems. (2021) (24)
- Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation. (2019) (23)
- Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes (2009) (23)
- Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly. (2015) (23)
- Synthetic Immunotherapeutics against Gram-negative Pathogens. (2018) (23)
- Effects of N-Glycan Composition on Structure and Dynamics of IgG1 Fc and Their Implications for Antibody Engineering (2017) (23)
- An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins. (2012) (22)
- Molecular dynamics simulations of glycoproteins using CHARMM. (2015) (22)
- Design, solid-phase synthesis, and evaluation of a phenyl-piperazine-triazine scaffold as α-helix mimetics. (2014) (22)
- A repulsive electrostatic mechanism for protein export through the type III secretion apparatus. (2010) (21)
- Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern (2022) (21)
- Protegrin‐1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations (2010) (21)
- Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials (2021) (20)
- Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers. (2009) (20)
- Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. (2014) (20)
- Additive CHARMM36 Force Field for Nonstandard Amino Acids. (2021) (19)
- NMR-based simulation studies of Pf1 coat protein in explicit membranes. (2013) (19)
- Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function (2009) (18)
- Augmenting the antinociceptive effects of nicotinic acetylcholine receptor activity through lynx1 modulation (2018) (18)
- Structure of an EIIC sugar transporter trapped in an inward-facing conformation (2018) (18)
- Structural insight into phospholipid transport by the MlaFEBD complex from P. aeruginosa. (2021) (17)
- Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity (2013) (17)
- Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. (2015) (17)
- Molecular dynamics simulation strategies for protein-micelle complexes. (2016) (17)
- Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model. (2017) (17)
- Theory of Adaptive Optimization for Umbrella Sampling (2014) (16)
- Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. (2011) (16)
- Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating. (2011) (16)
- CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. (2017) (16)
- Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. (2015) (16)
- Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigens. (2020) (16)
- Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations. (2017) (15)
- Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies. (2015) (15)
- Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane (2020) (15)
- Assessing smectic liquid-crystal continuum models for elastic bilayer deformations. (2013) (15)
- ST‐analyzer: A web‐based user interface for simulation trajectory analysis (2014) (14)
- Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes (2022) (13)
- Mutually constructive roles of Ail and LPS in Yersinia pestis serum survival (2020) (13)
- CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field (2021) (13)
- Heterogeneity in non‐epitope loop sequence and outer membrane protein complexes alters antibody binding to the major porin protein PorB in serogroup B Neisseria meningitidis (2017) (13)
- Quantification of Drive-Response Relationships Between Residues During Protein Folding. (2013) (13)
- G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures. (2017) (13)
- GlyMDB: Glycan Microarray Database and analysis toolset (2019) (12)
- GS-align for glycan structure alignment and similarity measurement (2015) (12)
- CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER (2021) (12)
- Site-Specific Lipidation Enhances IFITM3 Membrane Interactions and Antiviral Activity. (2021) (11)
- CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations (2020) (11)
- Ligand-Binding Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates. (2019) (11)
- Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions. (2016) (11)
- Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein. (2016) (10)
- Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes. (2018) (10)
- A mechano-reactive coarse-grained model of the blood-clotting agent von Willebrand factor. (2019) (10)
- Langevin dynamics simulations of charged model phosphatidylinositol lipids in the presence of diffusion barriers: toward an atomic level understanding of corralling of PIP2 by protein fences in biological membranes (2014) (9)
- CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids (2021) (9)
- Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures (2020) (9)
- Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain (2017) (9)
- Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. (2015) (9)
- Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids. (2021) (9)
- Structural basis of neuropeptide Y signaling through Y1 receptor (2022) (9)
- Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy. (2015) (9)
- Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding (2018) (8)
- Developing Initial Conditions for Simulations of Asymmetric Membranes: A Practical Recommendation. (2021) (8)
- Escherichia coli O176 LPS structure and dynamics: A NMR spectroscopy and MD simulation study (2020) (8)
- Analysis of Lipid Order States and Domains in Lipid Bilayer Simulations. (2018) (8)
- Beta‐hairpin restraint potentials for calculations of potentials of mean force as a function of beta‐hairpin tilt, rotation, and distance (2009) (8)
- S-Palmitoylation and Sterol Interactions Mediate Antiviral Specificity of IFITMs. (2022) (8)
- Broadening Activity of Polymyxin by Quaternary Ammonium Grafting. (2020) (8)
- Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study. (2018) (8)
- Methotrexate recognition by the human reduced folate carrier SLC19A1 (2022) (8)
- Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin. (2019) (8)
- Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. (2017) (8)
- A Systematic Analysis of Protein-Carbohydrate Interactions in the PDB. (2020) (8)
- Structural Conservation and Effects of Alterations in T Cell Receptor Transmembrane Interfaces. (2018) (7)
- Systematic Assessment of Accessibility to the Surface of Staphylococcus aureus. (2021) (7)
- All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer (2022) (7)
- Conformationally flexible core-bearing detergents with a hydrophobic or hydrophilic pendant: Effect of pendant polarity on detergent conformation and membrane protein stability. (2021) (7)
- Conformational states of the cytoprotective protein Bcl-xL (2020) (7)
- Influences of Vibrio cholerae Lipid A Types on LPS Bilayer Properties. (2021) (7)
- Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies (2021) (6)
- Molecular Simulation and Biochemical Studies Support an Elevator-type Transport Mechanism in EIIC. (2017) (6)
- Quantitative Characterization of Cholesterol Partitioning between Binary Bilayers. (2018) (6)
- A novel strategy to determine protein structures using exclusively residual dipolar coupling (2008) (6)
- Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP2 (2022) (6)
- Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination (2007) (6)
- Site-specific lipidation enhances IFITM3 membrane interactions and antiviral activity (2020) (6)
- CHARMM-GUI Martini Maker for Coarse-Grained Simulations (2015) (6)
- Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes. (2021) (6)
- First Step Towards Glycan Modeling: Charmm-Gui Glycan Reader and Glycan Database (2011) (6)
- Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids (2020) (6)
- Calcium and hydroxyapatite binding site of human vitronectin provides insights to abnormal deposit formation (2020) (6)
- CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation (2016) (5)
- CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface (2010) (5)
- CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement (2021) (5)
- Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes (2018) (5)
- Dynamics and Interactions of GPI-Linked Lynx1 Protein with/without Nicotinic Acetylcholine Receptor in Membrane Bilayers. (2020) (5)
- Transmembrane motions of PglB induced by LLO are coupled with EL5 loop conformational changes necessary for OST activity (2017) (5)
- U‐shaped caveolin‐1 conformations are tightly regulated by hydrogen bonds with lipids (2019) (5)
- Differential interactions between human ACE2 and spike RBD of SARS-CoV-2 variants of concern (2022) (4)
- Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS‐CoV‐2 variants of concern (2022) (4)
- Foldable detergents for membrane protein study: Importance of detergent core flexibility in protein stabilization. (2022) (4)
- S-palmitoylation and sterol interactions mediate antiviral specificity of IFITM isoforms (2021) (4)
- Cooperativity in Proteasome Core Particle Maturation (2020) (4)
- CHARMM‐GUI high‐throughput simulator for efficient evaluation of protein–ligand interactions with different force fields (2022) (4)
- CHARMM-GUI Ligand Reader & Modeler (2017) (4)
- Preferred Conformations of Lipooligosaccharides and Oligosaccharides of Moraxella catarrhalis. (2020) (4)
- Evolutionary balance between foldability and functionality of a glucose transporter (2022) (3)
- Correction to "Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen". (2021) (3)
- Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation Between Binary Bilayers. (2019) (3)
- St-Analyzer: A Web-Based User Interface for Simulation Trajectory Analysis (2014) (3)
- Exploring Protein-Lipid Interactions using Gramicidin a as a Model System (2013) (3)
- Molecular Basis of Aqueous-like Activity of Lipase Treated with Glucose-Headed Surfactant in Organic Solvent. (2018) (3)
- Stalis: A Computational Method for Template‐Based Ab Initio Ligand Design (2019) (3)
- CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids (2021) (3)
- CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site (2021) (3)
- CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle Simulations (2014) (2)
- Molecular Dynamics Simulation on thermodynamic and Structural Properties of Liquid Hydrocarbons : Normal Alkanes (1994) (2)
- Charmm-GUI Membrane Builder with Glycolipids and Lipopolysaccharides (2018) (2)
- Molecular Dynamics Simulation, 31P-NMR Spectroscopy, and Microelectrophoretic Studies of Cardiolipin Bilayers (2012) (2)
- Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies (2021) (2)
- CHARMM-GUI Synthetic Polymer Modeler for Modeling and Simulation of Synthetic Polymers (2019) (2)
- Web-Based Interface for Brownian Dynamics Simulation of Ion Channels and Its Application to Vdac (2011) (2)
- CHARMM Gui Membrane Builder Updates (2015) (2)
- Transmembrane motions of PglB induced by LLO are coupled with EL5 loop conformational changes necessary for OST activity. (2017) (2)
- Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane. (2020) (2)
- Molecular Dynamics Studies: The Effect of Phosphorylation in Saccharide Transporter System (2014) (1)
- From Molecular Dynamics to Supramolecular Organization: The Role of PIM Lipids in the Originality of the Mycobacterial Plasma Membrane (2022) (1)
- Conformational rearrangements in the sensory RcsF/OMP complex mediate signal transduction across the bacterial cell envelope (2023) (1)
- Pore Dilation in C-Type Inactivation of Potassium Channels (2010) (1)
- Molecular Dynamics Simulation Studies of Cardiolipin Bilayers (2011) (1)
- Langevin Dynamics Simulations of Protein Fencing of PIP2 (2012) (1)
- CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation (2023) (1)
- Revisiting Hydrophobic Mismatch with Free Energy Calculations of Transmembrane Helix Tilting (2010) (1)
- Automatic Assignment of Bonded Force Field Parameters for Small Molecules Using Machine Learning (2019) (1)
- Correction to "Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern". (2022) (1)
- Modulation of TRPV2 by endogenous and exogenous ligands: A computational study (2022) (1)
- Implicit Solvent Force-Field Optimization (2010) (1)
- CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods (2022) (1)
- A Molecular Dynamics Simulation Study of Outer Membrane Phospholipase a (OMPLA) Structure and Dynamics in an Asymmetric Lipopolysaccharide Membrane (2014) (1)
- Ion Channel Regulation by Lipid Bilayers: Theory & Simulation of Deformed Membranes around Gramicidin A (2015) (1)
- Bacterial Outer Membranes and Interactions with Membrane Proteins (2015) (1)
- NMR characterization of hydrophobic collapses in amyloidogenic unfolded states and their implications for amyloid formation. (2010) (1)
- Molecular basis of polyspecific drug binding and transport by OCT1 and OCT2 (2023) (1)
- FORMALISMS AND APPLICATIONS OF HELICAL RESTRAINT POTENTIALS (2008) (1)
- Don’t Fence Me in: Evidence for a ‘fence’ that Impedes the Diffusion of PIP2 Into and Out of Nascent Phagosomes in Macrophages (2010) (1)
- Protegrin-1 Orientation in Membrane Bilayers: Insights from Potential of Mean Force Calculations as A Function of Its Tilt and Rotation Angles (2010) (1)
- Assessment of Membrane Deformation Continuum Elastic Models Based on Molecular Simulations of Gramicidin A (2012) (1)
- Modeling and Simulation of Outer Membrane Proteins in Pseudomonas Aeruginosa Outer Membranes (2018) (1)
- Molecular Condensate in a Membrane: A Tugging Game between Hydrophobicity and Polarity with Its Biological Significance. (2022) (1)
- Improved Charmm Force Field for Polyunsaturated Fatty Acid Chains, a Study on DAPC Membranes (2013) (1)
- Author Correction: Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials (2021) (1)
- G-Losa: An Efficient Computational Tool for Local Structure-Centric Biological Studies (2015) (0)
- Molecular architecture of the Gαi-bound TRPC5 ion channel (2023) (0)
- Effects of N-Glycan Composition on Structure and Dynamics of IgG1 Fc and Their Implications for Antibody Engineering (2017) (0)
- Characterization of Pure Lipid Bilayers using Molecular Dynamics Simulations (2014) (0)
- CHARMM-GUI Enhanced Sampler for molecular dynamics simulations with collective variables and various enhanced sampling methods (2022) (0)
- Author Correction: Structural basis of neuropeptide Y signaling through Y1 receptor (2022) (0)
- Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations (2022) (0)
- CHARMM-GUI Implicit Solvent Modeler for simulation with various implicit solvent models in different simulation programs (2022) (0)
- T cell and B cell antigen receptors share a conserved core transmembrane structure. (2022) (0)
- Structure and Function of a Phosphorylation-Coupled Saccharide Transporter (2014) (0)
- Molecular Dynamics Simulation Studies of the Interferon-Induced Transmembrane Protein (IFITM3) (2019) (0)
- Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 having N-Glycans and Heparan Sulfates in Membranes (2017) (0)
- Cryo-EM structure determination of the human reduced folate carrier SLC19A1 in complex with methotrexate. (2023) (0)
- A (Passive to Active) Chaser: NMR and MD of Membrane Proteins (2018) (0)
- Binding Free Energies of Piezo1 Channel Agonists at Protein-Membrane Interface (2022) (0)
- Molecular Dynamics Studies of Lipid I and Lipid II in Various of Lipid Bilayer Environments (2015) (0)
- Study of the behavior of triacylglycerols in membrane bilayers and the formation of lipid droplets using all-atom molecular dynamics simulations (2022) (0)
- Mechanisms and Energetics of Protein/Peptide Interactions in Biological Membranes (2009) (0)
- Alternate approaches for simulating a reduced model of a transmembrane molecular pore with explicit mobile ions and continuum dielectric solvent include the dynamic lattice (2011) (0)
- Structure of Apo HasAp from Pseudomonas aeruginosa to 1.55A Resolution (2010) (0)
- Methotrexate recognition by the human reduced folate carrier SLC19A1. (2023) (0)
- Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding (2018) (0)
- Charmm-Gui NMR Structure Calculator: A Web-Based Tool for Calculating Biomolecular NMR Structures (2019) (0)
- Computational Study of Transmembrane Domain of Cytokine Receptor Family (2009) (0)
- Window Exchange Umbrella Sampling Molecular Dynamics Simulations for Transmembrane Helix Assembly (2012) (0)
- A Molecular Dynamics Simulation Study of Lipid-Linked Peptidoglycan Precursors in Lipid Bilayers (2014) (0)
- Lipoprotein sorting to the cell surface via a crosstalk between the Lpt and Lol pathways during outer membrane biogenesis (2022) (0)
- Molecular Simulation Studies of E. Coli O171, O175, and O181 LPS and V. Cholerae O1 LPS Symmetric Bilayers (2019) (0)
- Effect of Extrinsic Constraints on Lipid Bilayers (2011) (0)
- Mechanism of Substrate Binding and Lipid Modulation in Bile Acid Transporters (2021) (0)
- PG-1 Orientation in Lipid Bilayers: Insights from Molecular Dynamics Simulations and Calculations of Potentials of Mean Force as a Function of Its Tilt Angle (2009) (0)
- Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes (2018) (0)
- Investigation of the C-terminal domain of Caveolin-1 through molecular dynamics simulations (2022) (0)
- CHARMM Molecular Dynamics of the Blood Group Glycolipids in Popc Lipid Bilayer (2016) (0)
- Properties of Lipid a Bilayers Analyzed by Molecular Dynamics Simulations (2011) (0)
- CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations. (2023) (0)
- Computer-Aided Drug Design Utilizing Structure Templates Identified by Local Structure Alignment (2013) (0)
- CHARMM-GUI high-throughput simulator (2022) (0)
- Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues. (2016) (0)
- Absolute Binding Free Energy Calculations to Improve the Accuracy of Near-Native Ligand Pose Predictions (2012) (0)
- Modeling and Simulations of Glycosphingolipids Determining A, B, and O Blood Groups (2015) (0)
- Suppression of Lung Cancer Malignancy by Micellized siRNA through Cell Cycle Arrest (2023) (0)
- Protein Dynamics and Ion Traffic in Bacterioferritin Function: A Molecular Dynamics Simulation Study on wild‐type and Mutant Pseudomonas Aeruginosa BfrB (2016) (0)
- Molecular Dynamics Simulation Studies of Interactions of E. coli-K12 with OmpF in Outer Membranes: Effects of LPS Structures on Monoclonal Antibodies Binding (2015) (0)
- CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. (2023) (0)
- Molecular Dynamics Studies Support Elevator Type Transport Mechanisms in the Glucose EIIC Superfamily Transporters (2017) (0)
- Crystal Structure of an EIIC Trapped in an Inward-Facing Conformation (2018) (0)
- Modeling and Simulation of Outer Membranes with LPS, ECAs, and CPs (2019) (0)
- One small step toward all-atom modeling and simulation of the mycobacteria cell envelope (2022) (0)
- How CLC Chloride Transporter Folds (2018) (0)
- Interactions of human reduced folate carrier SLC19A1 with folates and antifolates. (2023) (0)
- An Analysis of Flat-Crack in Homogeneous Anisotropic Solids Considering Non-Singular Term (2000) (0)
- Sialic Acid Transport in E. coli: Role of Outer Membrane Porin NanC (2011) (0)
- Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III (2017) (0)
- Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane. (2023) (0)
- Effect of Asymmetry on Bilayer Membrane Systems (2015) (0)
- Structural Modeling of Human Growth Hormone Receptor using Computational Simulations and NMR Spectroscopy (2013) (0)
- Molecular Dynamics Studies for the Sugar Transportation Mechanism in Phosphotransferase Systems (PTSS) (2015) (0)
- Molecular Mechanism of Ligand-Induced TRPV2 Channel Activation (2019) (0)
- a Computational Approach to Explore Protein Translocation Through Type III Secretion Apparatus (2010) (0)
- Molecular Dynamics Simulation Studies of Lipopolysaccharide Micelles (2016) (0)
- Exploring Hydrophobic Mismatch using Molecular Dynamics Simulations of Gramicidin A in Lipid Bilayers (2011) (0)
- Development of PDB cleaning script for charmm GUI error reduction (2022) (0)
- OPRLM: Orientations of proteins in realistic lipid membranes. (2023) (0)
- CHARMM-GUI multicomponent assembler for modeling and simulation of complex multicomponent systems (2022) (0)
- Modeling Polymer Interactions with Nanopores for DNA Sequencing and Proteomics Applications (2012) (0)
- Exploring Hydrophobic Mismatch's Impacts on Dissociation of Gramicidin a Channels using Molecular Dynamics Free Energy Simulations (2012) (0)
- Structural-Function Study of Membrane Proteins with Restrained-Ensemble and Dummy Spin-Label Molecular Dynamics Simulations (2016) (0)
- Molecular Modeling and Simulations of the Transmembrane Domain of Human Growth Hormone Receptor (2010) (0)
- Modeling, Ion Conductance, and Electrostatic Properties of the Protective Antigen Pore Structure of Anthrax Toxin (2013) (0)
- N-Glycan Structure Modeling and in Silico Glycosylation: Template-Based Structure Prediction of Carbohydrate Structures of Glycoconjugates (2013) (0)
- Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides (2023) (0)
- Determining Vitronectin's Role in Forming the Hallmark of Age-Related Macular Degeneration (2021) (0)
- Hard to Fence You in: Computational Approaches to Explore the Hypothesis that Actin Filaments Impede PIP2 Diffusion in Membranes (2010) (0)
- Computational Studies of Membrane Protein Based on NMR Observables (2013) (0)
- Computational Characterization of DMPI and DMPI(4)P Head Groups (2011) (0)
- Transmembrane Helix Orientation and Dynamics Examined by Ensemble Dynamics with Solid-State NMR Observables and Potential of Mean Force Calculations (2010) (0)
- An Experimental Study on Fatigue Crack Growth of Cold-Expanded and Ring-Indented Holes on Both Sides (1998) (0)
- A Repulsive Electrostatic Mechanism For Protein Translocation Through Type III Secretion System: Insights From Pulling Simulations Of MxiH Across The Needle Apparatus Of Shigella Flexneri (2009) (0)
- NMR-Based Explicit Ensemble Dynamics Simulations of Membrane Protein (2014) (0)
- Window Exchange Umbrella Sampling to Enhance Conformational Sampling and Quantify Energetics in Transmembrane Helix Assembly (2013) (0)
- Structural changes of Gap junction visualized in simulation utilizing a double membrane (2022) (0)
- Molecular dynamics simulation studies of human DGAT1 and its substrates, acyl-CoA and diacylglycerol (2022) (0)
- Molecular Dynamics Simulations of 38 Types of Ganglioside in Homoegneous Membrane Bilayers (2017) (0)
- Molecular Dynamics Simulation Studies of Membrane Bilayers of Lipid a from Various Gram-Negative Bacteria (2016) (0)
- Transport Mechanism of the EIIC Glucose Superfamily of Transporters (2016) (0)
- Molecular Dynamics Simulations of Lipid-Linked Oligosaccharide in Membrane Bilayers (2013) (0)
- CHARMM-GUI mycobacterial lipid modeler and its incorporation into membrane builder (2022) (0)
- Elevator-Like Mechanism of Transport in the EIIC Glucose Superfamily of Transporters (2017) (0)
- All-Atom Simulation and Continuum Elastic Theory of Gramicidin a in Binary Component Lipid Bilayers (2014) (0)
- TRPV2 modulation by endogenous lipid and exogenous ligand (CBD) (2022) (0)
- Cytotoxicity of silver nanoparticles in the presence of gram-negative bacterial outer membranes: a molecular dynamics simulation study (2022) (0)
- Modeling and simulation of fully-glycosylated full-length HIV envelope protein embedded in a viral membrane (2022) (0)
- A Thermodynamic Discrimination of Efficacy of GPCR Ligands using Absolute Binding Free Energy Calculations (2014) (0)
- CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in LPS (2020) (0)
- Caveolin in Bilayers: Can the Intramembrane U-Shaped Conformation Really Exist (2014) (0)
- Probing Cholesterol Dependent Lipid Properties Using Molecular Dynamics Simulations of BODIPY-PC in Explicit DMPC and DPPC Membranes (2010) (0)
- A Structural Recognition Mechanism Study of MARCH and its Substrate (2012) (0)
- Glycan Builder for in Silico Glycosylation: Template-Based Structure Prediction of Carbohydrate Structures of Glycoconjugates (2012) (0)
- Evaluation of the Stress Intensity Factor for a Crack in Bimaterial Plate by the Boundary Method (1992) (0)
- CHARMM-GUI Molecular Dynamics Simulations of the Neo-Lacto Series in a Popc Bilayer (2016) (0)
- Experimentally Guided Computational Methods Yield Highly Accurate Insights into Transmembrane Interactions within the T Cell Receptor Complex. (2020) (0)
- Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study (2023) (0)
- All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed state (2021) (0)
- Function, Property, and Interaction of Archaeal Lipids: A Molecular Dynamics Simulation Study (2018) (0)
- Induced fit docking workflow based on charmm-gui modules: LBS Finder & Refiner and High-Throughput Simulator (2022) (0)
- Comparison of Lipid Monolayers and Bilayers by Comparative Molecular Dynamics Simulations of a Lipid-Like Dye Molecule (2010) (0)
- Vitronectin hemopexin-like domain with DHPC (2020) (0)
- Turning on the Human Growth Hormone Receptor: A Computational Study on its Structure and Activation Mechanism (2012) (0)
- Comparison of different force field combinations for ligand binding free energy calculations with amber (2022) (0)
- Developing initial conditions for simulations of asymmetric membranes: a practical recommendation (2022) (0)
- Supramolecular organisation and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane. (2023) (0)
- Analysis of Lipid Domains in Bilayer Simulations using Observables for Lipid Packing (2017) (0)
- CHARMM-GUI Lecture Series on Molecular Modeling and Simulation (2018) (0)
- Molecular Dynamics Simulations of Caveolin-1 in Membrane Bilayers (2013) (0)
- Fatigue Crack Growth Retardation Using Ring Indentation (2003) (0)
- Calcium-induced environmental adaptability of the blood protein vitronectin (2022) (0)
- Structure of dimeric holo HasAp H32A Mutant from Pseudomonas aeruginosa to 1.20A Resolution (2010) (0)
- Investigation of Signal Transduction through the HAMP Domain from Molecular Dynamics Simulations (2009) (0)
- Charmm-Gui Ligand Binder for Relative Binding Free Energy Calculations (2019) (0)
- CHARMM-GUI Nanomaterial Modeler: extension to ligand-protected nanomaterials (2022) (0)
- Biophysical characterization of lynx‐nicotinic receptor interactions using atomic force microscopy (2021) (0)
- Molecular Dynamics Simulation Studies of Polymyxin B Derivatives in Homogeneous E. coli K12 Bilayers (2018) (0)
- Glycan Structure Modeling and Simulation (2019) (0)
- Ensemble Dynamics with Orientational NMR Restraints in Solution and Membrane Environments (2009) (0)
- Introduction of Membrane Analyzer and Updates of Membrane Builder (2013) (0)
- Quantitative Characterization of Membrane Protein-Lipid Interactions (2014) (0)
- Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane (2020) (0)
- Molecular Dynamics Simulations of Lipid-Linked Oligosaccharides in Lipid Bilayers (2014) (0)
- Quantifying the Drive-Response Relationships between Residues in Protein Folding (2013) (0)
- Rationale design of novel PIEZO1 modulators. (2023) (0)
- CHARMM-GUI FF-Converter and Input Generator for support of various force fields and simulation programs (2022) (0)
- Molecular Dynamics Simulations of 41 Types of Ganglioside in Membrane Bilayers (2016) (0)
- Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling. (2022) (0)
- CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs. (2022) (0)
- Computational Toolset for Glycoconjugate Modeling and Simulation (2018) (0)
- Protocol and Validation of CHARMM-GUI Hex Phase Builder (2017) (0)
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