Keywords: Protein engineering; Truncated amylase; High pressure; Gromacs; Malto-oligosaccharides;
مقالات ISI (ترجمه نشده)
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Keywords: Soybean trypsin inhibitor; Ramachandran spectroscopy; Root mean square deviation; GROMACS; Hydrophobic effect;
Keywords: Molecular dynamics simulation; Gromacs; Amylose; Linoleic acid; Stearic acid; Complexation;
Keywords: Protein conformation; Charged droplet; Charged residue model; Ion mobility spectrometry; Gromacs;
Keywords: ADR; Adriamycin; BD; Brownian dynamics; CG; Coarse-grained; CMC; Critical micelle concentration; CUDA; Compute unified device architecture; DDFT; Dynamic density functional theory; DFT; Density functional theory; DLS; Dynamic light scattering; DMFT; Dynam
Keywords: Ã
; Angstrom; AFM; atomic force microscopy; AMBER; Assisted Model Building and Energy Refinement R. Salomon-Ferrer, D.A. Case, R.C. Walker, An overview of the Amber biomolecular simulation package, WIREs Comput. Mol. Sci. 3 (2012) 198-210; BSA; Bovine s
Keywords: Molecular dynamics; GROMACS; Electrophysiology; Ion channels; Conductance; Selectivity;
Keywords: RMSD; root mean square deviation; MD; molecular dynamics; GROMACS; groningen machine for chemical simulations; Protein modeling; Protein design; Molecular dynamics simulations; In silico mutation analysis;
Keywords: Molecular dynamics; Hybrid Monte Carlo; Multi-stage integrators; Velocity Verlet; Adaptive integration; GROMACS;
Keywords: Chlorhexidine; DMPC; Neutron diffraction; Slipids; NMR; GROMACS;
Keywords: Protein engineering; Truncated amylase; Gromacs; C-terminal;
Keywords: Lipopolysaccharide; POPE; MARTINI; Coarse grain; GROMACS; P. aeruginosa; Molecular dynamics
LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments
Keywords: Molecular dynamics; Neutron scattering; Correlation function; LAMMPS; GROMACS; VASP;
Understanding domain movements and interactions of Pseudomonas aeruginosa lipase with lipid molecule tristearoyl glycerol: A molecular dynamics approach
Keywords: Pseudomonas aeruginosa lipase; Molecular dynamics simulation; Lipid lipase interaction; Lid; GROMACS;
Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains' pathogenicity level
Keywords: Intramolecular Energies; Molecular modeling; Helicobacter pylori CagA; FoldX; Cluspro; Gromacs; PIC;
Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective
Keywords: HIV-1; Vpu; Secondary structure; HAD; Molecular dynamics; Gromacs; Amyloidogenicity; Neurodegenerative;
G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket
Keywords: G-score; Population density; Molecular dynamics; GROMACS; BACE1; Reduced amide; Tertiary carbinamine; Hydroxyethylamine; Protonation state; Alzheimer; TMoLiC;
Computational elucidation of novel antagonists and binding insights by structural and functional analyses of serine hydroxymethyltransferase and interaction with inhibitors
Keywords: SHMT; Serine hydroxymethyltransferase; Ld; Leishmania donovani; PLP; Pyridoxal phosphate; THF; Tetrahydrofolate; TS; Thymidylate synthase; PDB; Protein Data Bank; NCBI; National Center for Biotechnology Information; DOPE; Discrete optimized protein energy
E7 oncoprotein of human papillomavirus: Structural dynamics and inhibitor screening study
Keywords: HPV; Human papillomavirus; pRB; Phosphorylated Retiboblastoma; 3D; Three dimensional; MoRFs; Molecular recognition features; DNA; Deoxyribo nucleic acid; CRs; Conserved regions; IDPs; Intrinsically disordered proteins; CD-HIT; Cluster database at high ide
Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations
Keywords: Porcine reproductive and respiratory virus; PRRSV; nsp4; Catalytic triad; Molecular dynamics; Principle component analysis; GROMACS;
A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process
Keywords: BACE1; Hydroxyethylamine; Flap; PM7; MOPAC; Interaction energy; GROMACS; Molecular dynamics;
Structural analysis and insight into Zika virus NS5 mediated interferon inhibition
Keywords: ZIKV; Zika virus; NS5; non-structural protein 5; SIAH2; seven in absentia homolog 2; STAT2; Signal Transducer and Activator of Transcription 2; MTase; methyltransferase; IFN; interferon; IRF9; Interferon Regulatory Factor 9; ISGF3; Interferon-Stimulated G
Martini straight: Boosting performance using a shorter cutoff and GPUs
Keywords: Gromacs; Coarse-Grain; Verlet neighbor search; Lennard-Jones;
Determination of the protonation state for the catalytic dyad in β-secretase when bound to hydroxyethylamine transition state analogue inhibitors: A molecular dynamics simulation study
Keywords: Alzheimer’s disease (AD); Protonation state; Aspartatic dyad; BACE1; Hydroxyethylamine (HEA); Gromacs
Easy creation of polymeric systems for molecular dynamics with Assemble!
Keywords: Polymeric mixture; Molecular dynamics; Gromacs; Simulation preparation;
A molecular dynamics study of the BACE1 conformational change from Apo to closed form induced by hydroxyethylamine derived compounds
Keywords: Alzheimer's disease; Hydroxyethylamines; GROMACS; BACE1; Flap; Population density;
All-atom molecular dynamics simulations of lung surfactant protein B: Structural features of SP-B promote lipid reorganization
Keywords: SP-B; surfactant protein B; LS; lung surfactant; PC; phosphocholine; DPPC; 1,2-dipalmitoyl-sn-glycero-3-phosphocholine; PG; phosphatidylglycerol; POPC; 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; AA; all-atom; CG; coarse-grained; MD; molecular dynam
Thermostable chitinase II from Thermomyces lanuginosus SSBP: Cloning, structure prediction and molecular dynamics simulations
Keywords: LB; Luria Bertani; SSBP; Suren Singh Bernard Prior; cDNA; complementary deoxyribonucleic acid; RMSD; root mean square deviation; SignalP; signal peptide; MD; molecular dynamics; GROMACS; GROningen MAchine for Chemical Simulations; OPLS-AA/L; optimized pot
Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: Insights from molecular dynamics simulation
Keywords: Ethanol; Cosolute; Hoogsteen hydrogen bond; Gromacs;
Comparative structural and conformational studies on H43R and W32F mutants of copper-zinc superoxide dismutase by molecular dynamics simulation
Keywords: SOD1; fALS; W32F; H43R; Molecular dynamics; GROMACS;
Molecular modeling and molecular dynamics simulations of GPI 14 in Leishmania major: Insight into the catalytic site for active site directed drug design
Keywords: CL; cutaneous leishmaniasis; MCL; mucocutaneous leishmaniasis; VL; visceral leishmaniasis; LPG; lipophosphoglycan; GIPLs; glycoinositolphospholipids; GPI; glycosylphosphatidylinositol; iNOS; inducible nitric oxide synthase; NO; nitric oxide; PPG; proteoph
GMXPBSA 2.0: A GROMACS tool to perform MM/PBSA and computational alanine scanning
Keywords: Molecular dynamics simulation; Binding free energy; Virtual screening; GROMACS; Computational alanine scanning; MM/PBSA;
The Flexible Rare Event Sampling Harness System (FRESHS)
Keywords: Rare event sampling; Forward Flux Sampling (FFS); Stochastic Process Rare Event Sampling (SPRES); GROMACS; LAMMPS; ESPResSo; HPC; Chemical physics;
Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering
Keywords: RecX; RecA; Molecular dynamics; GROMACS; Small angle neutron scattering;
g_contacts: Fast contact search in bio-molecular ensemble data
Keywords: Range search; Molecular dynamics; Decomposition scheme; Gromacs;
Understanding the lid movements of LolA in Escherichia coli using molecular dynamics simulation and in silico point mutation
Keywords: Molecular dynamics; Lid movements; LolA; Lipoproteins; GROMACS; Escherichia coli;
Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein
Keywords: Monte Carlo; Molecular Dynamics; Enhanced sampling; GROMACS; Prion misfolding
Anopheles gambiae, Anoga-HrTH hormone, free and bound structure – A nuclear magnetic resonance experiment
Keywords: Anopheles gambiae; Anoga-HrTH; Molecular dynamics; GROMACS; AUTODOCK
Structural effect of the L16Q, K50E, and R53P mutations on homeodomain of pituitary homeobox protein 2
Keywords: PITX2 homeodomain; Gromacs; Molecular dynamics simulation; Rieger syndrome; Mutation; DNA-binding;
Mechanism of structural transformations induced by antimicrobial peptides in lipid membranes
Keywords: AMP; AntiMicrobial Peptide; PG-1; Protegrin-1; AFM; Atomic Force Microscopy; DHPC; 1,2-dihexanoyl-sn-glycero-3-phospho-choline; DMPC; 1,2-dimyristoyl-sn-glycero-3-phospho-choline; SDS; sodium-dodecyl-sulfate; DPC; dodecyl-phospho-choline; POPC; palmitoyl-
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics
Keywords: NMR; Nuclear Magnetic Resonance; MD; Molecular Dynamics; HMQC; Heteronuclear Multiple Quantum Correlation; COSY; Correlation Spectroscopy; TOCSY; Total Correlation Spectroscopy; CD; Circular Dichroism; GROMOS 96; Groningen MoleculaR Simulation; GROMACS; G
Structure of the interface between water and self-assembled monolayers of neutral, anionic and cationic alkane thiols
Keywords: Dipole moment; Surface; Gold (111); Gromacs; Tilt angle;
Molecular dynamics simulations of human and dog gastric lipases: Insights into domain movements
Keywords: Gastric lipase; Acidic pH; Molecular dynamics; Lid; Mobile domain; GROMACS
Characterization of the conformational ensemble from bioactive N-acylhydrazone derivatives
Keywords: Conformational analysis; GROMACS; LASSBio-294; Molecular dynamics; N-Acylhydrazone
Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions
Keywords: GPR40; Molecular docking; Molecular dynamics simulation; AutoDock; GROMACS
Statistical thermodynamics of biomembranes
Keywords: GROMACS; Dimethylsulfoxide; Lipid bilayer structure; Mass density profiles; Radial distribution function; Water orientation profile; Deuterium order parameter
g_permute: Permutation-reduced phase space density compaction
Keywords: 02.60.Pn; 02.70.-c; 02.70.Ns; 05.10.-a; 87.10.-e; 87.10.Tf; 05.70.-a; 65.40.gdPermutation reduction; Solvent entropy; All-atom (fully atomistic) molecular dynamics simulations; GROMACS; Compacted configuration space density
Solution conformations of an insect neuropeptide: Crustacean cardioactive peptide (CCAP)
Keywords: DPC; dodecylphosphocholine; NMR; nuclear magnetic resonance; DSS; 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt; TSP; 3-(trimethylsilyl)-propionic acid-D4 sodium salt; DMSO; dimethyl sulfoxide; 2D; two-dimensional; NOE; nuclear Overhauser effect; NOE
A study of local effect and global effect on the microthermal bio-flows by molecular dynamics
Keywords: Alanine; GROMACS; MD; Thermal bio-flow
Long-range interactions and parallel scalability in molecular simulations
Keywords: Molecular simulations; Parallel computing; Electrostatics; Lipid membranes; GROMACS