Cloud-HTMD
A cloud application platform for rational drug discovery using high throughput molecular dynamics.
European SME innovation Associate (H2020-INNOSUP-02-2016, Grant Agreement 739649)
Research
Methods, publications and open code.
Explore the peer reviewed and preprint research behind Acellera's biomolecular simulation, machine learning and drug discovery software.
01 How we work
Applied research, with partners, in the open
Since 2006 we have supported applied research into biomolecular simulation methods and machine learning predictors through agreements with academic institutions. The results go into journals with DOIs, and much of the code goes onto GitHub.
For routine academic use, start with HTMD or the free research tools on Open PlayMolecule. Institutions with a defined scientific question, project lead and funding context can propose a research collaboration.
Python ecosystem
ACEMD® Toolkit brings together the ACEMD engine, HTMD, MoleculeKit, TorchMD and TorchMD-Net, AceFF and related components for molecular physics and simulation. Much of the ecosystem is open source.
Open access
open.playmolecule.org hosts a molecular viewer, preparation tools and affinity predictors, free to use in the browser.
Licence
Licensing varies by component. The ACEMD engine is free for non commercial research and requires a licence for commercial use. See ACEMD Toolkit.
02 Publications
Publications, searchable
75
publications and preprints listed
Open
code and browser based research tools
2006
Acellera founded
Showing 0 of 0 publications.
-
Evaluating Electrostatic Embedding MLIP/MM for Relative Binding Free Energy Calculations
Protein-Ligand Binding View publication
-
Structure-guided molecular design with contrastive 3D protein-ligand learning
Applications View publication
-
Thermodynamics-Informed Accurate pKa Prediction and Protonation State Generation in PlayMolecule AI
Applications View publication
-
AceFF: A State-of-the-Art Machine Learning Potential for Small Molecules
Molecular Simulations View publication
-
Speak to a Protein: An Interactive Multimodal Co-Scientist for Protein Analysis
Applications View publication
-
Navigating protein landscapes with a machine-learned transferable coarse-grained model
Molecular Simulations View publication
-
QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials
Protein-Ligand Binding View publication
-
Broadening the Scope of Neural Network Potentials through Direct Inclusion of Additional Molecular Attributes
Molecular Simulations View publication
-
On Machine Learning Approaches for Protein-Ligand Binding Affinity Prediction
Protein-Ligand Binding View publication
-
PlayMolecule pKAce: Small Molecule Protonation through Equivariant Neural Networks
Applications View publication
-
PlayMolecule Viewer: a toolkit for the visualization of molecules and other data
Applications View publication
-
TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations
Applications View publication
-
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery
Applications View publication
-
Enhancing Protein–Ligand Binding Affinity Predictions Using Neural Network Potentials
Applications View publication
-
Openmm 8: Molecular dynamics simulation with machine learning potentials
Molecular Simulations View publication
-
NNP/MM: Accelerating molecular dynamics simulations with machine learning potentials and molecular mechanics
ACEMD/HTMD/AceCloud View publication
-
Top-Down Machine Learning of Coarse-Grained Protein Force Fields
Molecular Simulations View publication
-
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series
Applications View publication
-
Machine learning coarse-grained potentials of protein thermodynamics
Molecular Simulations View publication
-
Machine Learning Small Molecule Properties in Drug Discovery
Molecular Simulations View publication
-
TorchRL: A data-driven decision-making library for PyTorch
Applications View publication
-
Structure based virtual screening: Fast and slow
Protein-Ligand Binding View publication
-
PlayMolecule glimpse: Understanding protein–ligand property predictions with interpretable neural networks
Applications View publication
-
TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials
Applications View publication
-
TorchMD: A deep learning framework for molecular simulations
Applications View publication
-
AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations
Applications View publication
-
Small molecule modulation of intrinsically disordered proteins using molecular dynamics simulations
Applications View publication
-
Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations
Applications View publication
-
SkeleDock: a web application for scaffold docking in PlayMolecule
Applications View publication
-
PlayMolecule CrypticScout: predicting protein cryptic sites using mixed-solvent molecular simulations
Applications View publication
-
Shape-based generative modeling for de novo drug design
Applications View publication
-
Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots
Applications View publication
-
DeltaDelta neural networks for lead optimization of small molecule potency
Applications View publication
-
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks
Applications View publication
-
From target to drug: generative modeling for the multimodal structure-based ligand design
Applications View publication
-
A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning
Applications View publication
-
PathwayMap: molecular pathway association with self-normalizing neural networks
Applications View publication
-
PlayMolecule BindScope: Large scale CNN-based virtual screening on the web
Applications View publication
-
Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs
Protein-Ligand Binding View publication
-
Molecular-simulation-driven fragment screening for the discovery of new CXCL12 inhibitors
Fragment Based Drug Discovery View publication
-
K deep: protein–ligand absolute binding affinity prediction via 3d-convolutional neural networks
Applications View publication
-
Drug discovery and molecular dynamics: methods, applications and perspective beyond the second timescale
Applications View publication
-
PlayMolecule ProteinPrepare: a web application for protein preparation for molecular dynamics simulations
Applications View publication
-
Optimizing Proteins and Ligands for Computerized Drug Discovery
Applications View publication
-
Dimensionality reduction methods for molecular simulations
Molecular Simulations View publication
-
DeepSite: protein-binding site predictor using 3D-convolutional neural networks
Applications View publication
-
High-throughput automated preparation and simulation of membrane proteins with HTMD
ACEMD/HTMD/AceCloud View publication
-
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Conformational Studies View publication
-
Binding kinetics in drug discovery
Protein-Ligand Binding View publication
-
Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme
Protein-Ligand Binding View publication
-
HTMD: high-throughput molecular dynamics for molecular discovery
ACEMD/HTMD/AceCloud View publication
-
The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor
Membrane Proteins View publication
-
Insights from fragment hit binding assays by molecular simulations
Fragment Based Drug Discovery View publication
-
AceCloud: molecular dynamics simulations in the cloud
ACEMD/HTMD/AceCloud View publication
-
Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation
Fragment Based Drug Discovery View publication
-
HTMD: A complete software workspace for simulation-guided drug design
ACEMD/HTMD/AceCloud View publication
-
Kinetic modulation of a disordered protein domain by phosphorylation
Conformational Studies View publication
-
Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations
Conformational Studies View publication
-
Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH
Applications View publication
-
On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations
ACEMD/HTMD/AceCloud View publication
-
Reranking docking poses using molecular simulations and approximate free energy methods
Molecular Simulations View publication
-
Identification of slow molecular order parameters for Markov model construction
ACEMD/HTMD/AceCloud View publication
-
Kinetic characterization of the critical step in HIV-1 protease maturation
Conformational Studies View publication
-
High-throughput molecular dynamics: the powerful new tool for drug discovery
Molecular Simulations View publication
-
Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase
Conformational Studies View publication
-
Visualizing the induced binding of SH2-phosphopeptide
Protein-Ligand Binding View publication
-
Optimized potential of mean force calculations for standard binding free energies
Applications View publication
-
A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A
Applications View publication
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Protein-Ligand Binding View publication
-
Explicit solvent dynamics and energetics of HIV‐1 protease flap opening and closing
Conformational Studies View publication
-
Induced effects of sodium ions on dopaminergic G-protein coupled receptors
Membrane Proteins View publication
-
High-throughput all-atom molecular dynamics simulations using distributed computing
Applications View publication
-
ACEMD: Accelerating biomolecular dynamics in the microsecond time scale
ACEMD/HTMD/AceCloud View publication
-
An implementation of the smooth particle mesh Ewald method on GPU hardware
Conformational Studies View publication
-
The impact of accelerator processors for high-throughput molecular modeling and simulation
Molecular Simulations View publication
03 Funded projects
International and EU funded projects
CCFBLD-CHEMO
Computer-Centric Fragment Based Ligand Discovery for the Development of candidate molecules targeting the chemkine system.
Nuclis d’Innovació Tecnològica 2014. Acció, Generalitat de Catalunya. Nuclis Transnacionals Programa Bilateral Catalunya-Israel, Project nr. RDIS14-1-0002. 2014-2016
HTMD
Feasibility assessment of a cloud application platform for rational drug design using high-throughput.
H2020 SME Instrument 2014, Grant Agreement nr. 674659. 2015
CompBioMed
A Centre of Excellence in Computational Biomedicine.
H2020-EINFRA-2015-1, Grant Agreement nr. 675451. 2016-2019
CompBioMed2
A Centre of Excellence in Computational Biomedicine.
H2020-INFRAEDI-02-2018, Grant Agreement nr. 823712. 2019-2023