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Comparez modèles biologiques, moteurs de docking et flux de calcul côte à côte. Filtrez par modèle d'accès, empreinte de calcul et catégorie pour parvenir à une table de décision exploitable en moins d'une minute.
| Attribut | ＋ Ajouter un outil | |||
|---|---|---|---|---|
| Category | Research Tooling & Frameworks | Scientific ML Libraries & Supporting Tools | Scientific ML Libraries & Supporting Tools | — |
| Subcategory | Molecular Dynamics Engines | Conventional or Statistical Baselines | Conventional or Statistical Baselines | — |
| Company | GROMACS Development Team | Research / method authors | Research / method authors | — |
| Access mode | Open Source | Confirm distribution and exact release | Confirm distribution and exact release | — |
| Licence conditions | LGPL-2.1 | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | — |
| Compute requirements | Multi-core CPU and NVIDIA/AMD GPU for accelerated PME electrostatics | Version and data dependent | Version and data dependent | — |
| Biological application | Biomolecular dynamics, membrane transport, protein folding, and drug-target residence time | Non enregistré | Non enregistré | — |
| Research workflow | PDB topology generation -> energy minimization -> equilibration -> production MD trajectory | Non enregistré | Non enregistré | — |
| Evidence level | Cited in over 30,000 peer-reviewed biophysics publications | PEER_REVIEWED_METHOD_OR_CONFERENCE | PEER_REVIEWED_METHOD_OR_CONFERENCE | — |
| Commercial eligibility | Permissive open source release | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | — |
| Price | Free Open Source | Verify access and licence | Verify access and licence | — |
| Availability ⓘ | Available via Bioconda and source compilation | Method paper or official documentation | Method paper or official documentation | — |
| Features | Unrivaled simulation throughput on modern x86/ARM CPUs and NVIDIA/AMD GPUs, Comprehensive support for standard force fields (AMBER, CHARMM, OPLS, GROMOS), Free energy calculation tools for relative binding affinity and alchemical transformations, Extensive trajectory analysis utilities for root-mean-square deviation, gyration, and hydrogen bonds | HMMER 3 scientific method, Query sequences or profile HMM and sequence database, Profile HMM hits and statistical homology significance | MMseqs2 scientific method, Amino acid queries and reference sequence database, Sequence matches, clusters and alignment results | — |
| Entry type | Open Source Software | Classical/statistical scientific method | Classical/statistical scientific method | — |
| AI role | Physical Molecular Dynamics Simulation | NON_AI_CLASSICAL | NON_AI_CLASSICAL | — |
| Input data | Non enregistré | Query sequences or profile HMM and sequence database | Amino acid queries and reference sequence database | — |
| Output data | Non enregistré | Profile HMM hits and statistical homology significance | Sequence matches, clusters and alignment results | — |
| Validation | Non enregistré | Published method scope; no independent BioAtlas execution or benchmark | Published method scope; no independent BioAtlas execution or benchmark | — |
| Type | Molecular dynamics simulation engine | Non enregistré | Non enregistré | — |
| Intended use | Non enregistré | Non enregistré | Non enregistré | — |
| Compatibility | Non enregistré | Non enregistré | Non enregistré | — |
| Manufacturer | GROMACS Team & KTH Royal Institute of Technology | Non enregistré | Non enregistré | — |
| Integration evidence | https://www.gromacs.org | Non enregistré | Non enregistré | — |
| Laboratory handoff | Validates dynamic conformational stability of designed protein candidates | Non enregistré | Non enregistré | — |