On the public citation graph

iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment

https://doi.org/10.1021/ci300524j
0 signed · 49 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/1096-987x(200012)21:16<1532::aid-jcc10>3.0.co;2-wopenalex-snapshot
Q-Chem 2.0: a high-performanceab initio electronic structure program package
inferredcites →https://doi.org/10.1002/bmb.2006.494034042644openalex-snapshot
Biomolecules in the computer: Jmol to the rescue
inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
Scalable molecular dynamics with NAMD
inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot
The Amber biomolecular simulation programs
inferredcites →https://doi.org/10.1002/jcc.21922openalex-snapshot
Quantum mechanically derived AMBER‐compatible heme parameters for various states of the cytochrome P450 catalytic cycle
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540141112openalex-snapshot
General atomic and molecular electronic structure system
inferredcites →https://doi.org/10.1002/med.20067openalex-snapshot
Combining docking and molecular dynamic simulations in drug design
inferredcites →https://doi.org/10.1006/jcph.1995.1039openalex-snapshot
Fast Parallel Algorithms for Short-Range Molecular Dynamics
inferredcites →https://doi.org/10.1007/s12038-012-9222-6openalex-snapshot
The ABCs of molecular dynamics simulations on B-DNA, circa 2012
inferredcites →https://doi.org/10.1016/j.cpc.2010.04.018openalex-snapshot
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
inferredcites →https://doi.org/10.1016/j.future.2005.10.005openalex-snapshot
BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis
inferredcites →https://doi.org/10.1016/j.str.2010.07.013openalex-snapshot
MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1039/b309040jopenalex-snapshot
Research applications of the Cambridge Structural Database (CSD)
inferredcites →https://doi.org/10.1080/08927020500067195openalex-snapshot
Collaborative grid infrastructure for molecular simulations: TheeMinerals minigrid as a prototype integrated compute and data grid
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/10.1093/database/baq033openalex-snapshot
Bookshelf: a simple curation system for the storage of biomolecular simulation data
inferredcites →https://doi.org/10.1093/nar/gkp456openalex-snapshot
PubChem: a public information system for analyzing bioactivities of small molecules
inferredcites →https://doi.org/10.1093/nar/gkp834openalex-snapshot
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
inferredcites →https://doi.org/10.1093/protein/gzn012openalex-snapshot
Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations
inferredcites →https://doi.org/10.1111/j.1432-1033.1977.tb11885.xopenalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1126/science.1157834openalex-snapshot
Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems
inferredcites →https://doi.org/10.1145/1273440.1250664openalex-snapshot
Anton, a special-purpose machine for molecular dynamics simulation
inferredcites →https://doi.org/10.1145/1364782.1364802openalex-snapshot
Anton, a special-purpose machine for molecular dynamics simulation
inferredcites →https://doi.org/10.1145/1925805.1925816openalex-snapshot
The SDSC storage resource broker
inferredcites →https://doi.org/10.1146/annurev-biophys-042910-155245openalex-snapshot
Biomolecular Simulation: A Computational Microscope for Molecular Biology
inferredcites →https://doi.org/10.1186/1471-2105-12-361openalex-snapshot
Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute
inferredcites →https://doi.org/10.1529/biophysj.104.045252openalex-snapshot
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps
inferredcites →https://doi.org/10.1529/biophysj.105.067397openalex-snapshot
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/spe.2732openalex-snapshot
EDISON‐DATA: A flexible and extensible platform for processing and analysis of computational science data
inferred← citeshttps://doi.org/10.1007/978-981-15-8936-2_12openalex-snapshot
Molecular Dynamics Simulation in Drug Discovery: Opportunities and Challenges
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00018openalex-snapshot
Simulation Foundry: Automated and F.A.I.R. Molecular Modeling
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00252openalex-snapshot
TMB Library of Nucleosome Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpca.6b10489openalex-snapshot
Computational Chemistry Data Management Platform Based on the Semantic Web
inferred← citeshttps://doi.org/10.1021/ci500173wopenalex-snapshot
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings
inferred← citeshttps://doi.org/10.1021/ci500469fopenalex-snapshot
Creating Context for the Experiment Record. User-Defined Metadata: Investigations into Metadata Usage in the LabTrove ELN
inferred← citeshttps://doi.org/10.1038/s41597-019-0177-4openalex-snapshot
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
inferred← citeshttps://doi.org/10.1080/1062936x.2015.1076515openalex-snapshot
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology
inferred← citeshttps://doi.org/10.1088/1742-6596/1036/1/012010openalex-snapshot
Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments
inferred← citeshttps://doi.org/10.1093/nar/gkad991openalex-snapshot
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort
inferred← citeshttps://doi.org/10.1093/nar/gkv1301openalex-snapshot
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
inferred← citeshttps://doi.org/10.1101/2024.12.03.626554openalex-snapshot
Integrated Database of Force-Field Parameters, Experimental Measurements and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1109/bibm.2016.7822610openalex-snapshot
A distributed and privatized framework for drug-target interaction prediction
inferred← citeshttps://doi.org/10.1109/mcse.2015.7openalex-snapshot
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
inferred← citeshttps://doi.org/10.1145/3007818.3007826openalex-snapshot
Design and implementation of a data-driven simulation service system
inferred← citeshttps://doi.org/10.1146/annurev-physchem-082120-041521openalex-snapshot
eScience Infrastructures in Physical Chemistry
inferred← citeshttps://doi.org/10.1186/1758-2946-6-4openalex-snapshot
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing
inferred← citeshttps://doi.org/10.1186/s13321-025-01082-5openalex-snapshot
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.