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A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/1097-0282(2000)56:4<257::aid-bip10029>3.0.co;2-wopenalex-snapshot
Development and current status of the CHARMM force field for nucleic acids
inferredcites →https://doi.org/10.1002/andp.19213690304openalex-snapshot
Die Berechnung optischer und elektrostatischer Gitterpotentiale
inferredcites →https://doi.org/10.1002/jcc.1078openalex-snapshot
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
inferredcites →https://doi.org/10.1002/jcc.20050openalex-snapshot
A method to obtain a near‐minimal‐volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot
The Amber biomolecular simulation programs
inferredcites →https://doi.org/10.1002/jcc.20341openalex-snapshot
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions
inferredcites →https://doi.org/10.1002/jcc.21035openalex-snapshot
Application of MDGRAPE‐3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems
inferredcites →https://doi.org/10.1002/jcc.21816openalex-snapshot
SwissParam: A fast force field generation tool for small organic molecules
inferredcites →https://doi.org/10.1002/prot.22702openalex-snapshot
Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein
inferredcites →https://doi.org/10.1007/978-94-009-6463-1_16openalex-snapshot
Molecular Dynamics Simulations: Techniques and Approaches
inferredcites →https://doi.org/10.1007/bf00355047openalex-snapshot
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
inferredcites →https://doi.org/10.1007/s10969-010-9084-9openalex-snapshot
The eNMR platform for structural biology
inferredcites →https://doi.org/10.1016/0010-4655(95)00042-eopenalex-snapshot
GROMACS: A message-passing parallel molecular dynamics implementation
inferredcites →https://doi.org/10.1016/0022-2836(87)90294-4openalex-snapshot
Structure of form III crystals of bovine pancreatic trypsin inhibitor
inferredcites →https://doi.org/10.1016/j.bpj.2010.05.005openalex-snapshot
Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water
inferredcites →https://doi.org/10.1016/j.jmgm.2005.12.005openalex-snapshot
Automatic atom type and bond type perception in molecular mechanical calculations
inferredcites →https://doi.org/10.1016/j.str.2005.11.014openalex-snapshot
Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
inferredcites →https://doi.org/10.1017/s0033583510000284openalex-snapshot
Biomolecular modeling and simulation: a field coming of age
inferredcites →https://doi.org/10.1021/bi00181a032openalex-snapshot
Two Crystal Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison with NMR
inferredcites →https://doi.org/10.1021/ct200196mopenalex-snapshot
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1021/ct9001015openalex-snapshot
Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility
inferredcites →https://doi.org/10.1021/ja0753546openalex-snapshot
Dynamics of B-DNA on the Microsecond Time Scale
inferredcites →https://doi.org/10.1021/ja9090353openalex-snapshot
Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/jp003919dopenalex-snapshot
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
inferredcites →https://doi.org/10.1021/jp077018hopenalex-snapshot
Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins
inferredcites →https://doi.org/10.1021/jp984217fopenalex-snapshot
The GROMOS Biomolecular Simulation Program Package
inferredcites →https://doi.org/10.1038/nprot.2010.32openalex-snapshot
The HADDOCK web server for data-driven biomolecular docking
inferredcites →https://doi.org/10.1063/1.2408420openalex-snapshot
Canonical sampling through velocity rescaling
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1063/1.469273openalex-snapshot
A generalized reaction field method for molecular dynamics simulations
inferredcites →https://doi.org/10.1063/1.480557openalex-snapshot
Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency
inferredcites →https://doi.org/10.1073/pnas.0811065106openalex-snapshot
Identification of two distinct inactive conformations of the β 2 -adrenergic receptor reconciles structural and biochemical observations
inferredcites →https://doi.org/10.1093/bioinformatics/bts139openalex-snapshot
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
inferredcites →https://doi.org/10.1103/physrevb.31.2643openalex-snapshot
Molecular-dynamics study of atomic motions in water
inferredcites →https://doi.org/10.1111/j.1432-1033.1995.293_1.xopenalex-snapshot
Structure of Amyloid A4‐(1–40)‐Peptide of Alzheimer's Disease
inferredcites →https://doi.org/10.1136/jnnp.2004.061911openalex-snapshot
Beyond the holy grail of motor symptoms: deep brain stimulation for Parkinson's disease
inferredcites →https://doi.org/10.1145/1654059.1654099openalex-snapshot
Millisecond-scale molecular dynamics simulations on Anton
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/cpe.3116openalex-snapshot
Standards‐based metadata management for molecular simulations
inferred← citeshttps://doi.org/10.1002/humu.23367openalex-snapshot
ERCC4 variants identified in a cohort of patients with segmental progeroid syndromes
inferred← citeshttps://doi.org/10.1007/978-1-4939-8891-4_16openalex-snapshot
In Silico Target Prediction for Small Molecules
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From Desktop to Supercomputer: Computational Fluid Dynamics Augmented by Molecular Dynamics Using MaMiCo and preCICE
inferred← citeshttps://doi.org/10.1007/s10723-012-9246-zopenalex-snapshot
WeNMR: Structural Biology on the Grid
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Hereditary coagulation factor VII deficiency caused by novel compound heterozygous mutations c.572-1G>A and c.1037A>C in a Chinese pedigree
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Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19?
inferred← citeshttps://doi.org/10.1016/j.molliq.2020.112870openalex-snapshot
Futuristic advance and perspective of deep eutectic solvent for extractive desulfurization of fuel oil: A review
inferred← citeshttps://doi.org/10.1021/acs.biochem.1c00408openalex-snapshot
Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00044openalex-snapshot
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00222openalex-snapshot
Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00615openalex-snapshot
Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins
inferred← citeshttps://doi.org/10.1021/ci500007nopenalex-snapshot
CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations
inferred← citeshttps://doi.org/10.1021/ct500159hopenalex-snapshot
The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations
inferred← citeshttps://doi.org/10.1021/jp311533popenalex-snapshot
Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic–Coarse-Grained Biomolecular Simulations
inferred← citeshttps://doi.org/10.1038/s41596-023-00885-wopenalex-snapshot
A practical guide to machine-learning scoring for structure-based virtual screening
inferred← citeshttps://doi.org/10.1074/jbc.ra118.002779openalex-snapshot
Profilin binding couples chloride intracellular channel protein CLIC4 to RhoA–mDia2 signaling and filopodium formation
inferred← citeshttps://doi.org/10.1080/00222348.2024.2403861openalex-snapshot
Nanoarchitectonics in Macromolecular Science: Integrating Molecular Dynamics with Smart Materials
inferred← citeshttps://doi.org/10.1080/07391102.2019.1705913openalex-snapshot
Identification of the potential dual inhibitor of protein tyrosine phosphatase sigma and leukocyte common antigen-related phosphatase by virtual screen, molecular dynamic simulations and post-analysis
inferred← citeshttps://doi.org/10.1101/147926openalex-snapshot
Glucose limitation in Lactococcus shapes a single-peaked fitness landscape exposing membrane occupancy as a constraint
inferred← citeshttps://doi.org/10.1104/pp.18.00268openalex-snapshot
Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection
inferred← citeshttps://doi.org/10.1109/iwsg.2014.21openalex-snapshot
Integration of eSBMTools into the MoSGrid Portal Using the gUSE Technology
inferred← citeshttps://doi.org/10.1109/tcbb.2017.2713362openalex-snapshot
A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer
inferred← citeshttps://doi.org/10.1111/jfbc.12728openalex-snapshot
Effect of chrysin omega‐3 and 6 fatty acid esters on mushroom tyrosinase activity, stability, and structure
inferred← citeshttps://doi.org/10.1186/1471-2105-15-292openalex-snapshot
Native structure-based modeling and simulation of biomolecular systems per mouse click
inferred← citeshttps://doi.org/10.1186/s13321-017-0243-xopenalex-snapshot
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations
inferred← citeshttps://doi.org/10.1186/s13568-018-0638-8openalex-snapshot
Engineering E. coli cell surface in order to develop a one-step purification method for recombinant proteins
inferred← citeshttps://doi.org/10.22323/1.162.0040openalex-snapshot
Extending WeNMR e-Infrastructure outside Europe
inferred← citeshttps://doi.org/10.3390/ijms141224514openalex-snapshot
CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations
inferred← citeshttps://doi.org/10.3390/jof8121281openalex-snapshot
Calcineurin Inhibitor CN585 Exhibits Off-Target Effects in the Human Fungal Pathogen Aspergillus fumigatus
inferred← citeshttps://doi.org/10.70675/d7833ec2zd4c5z47b6zb245zd5bb0c5e89eaopenalex-snapshot
Link between molecular composition, ultrastructure, and infectivity of Germiston viruses (GERV) derived from mammalian and mosquito cell lines
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