Rowan Docs

How to Cite Work Using Rowan

Any publication using Rowan should cite it as follows:

Rowan Scientific. https://www.rowansci.com (accessed yyyy-mm-dd).

Engines

Cite the engines, workflow methods, and models used in your work. References shared by several workflows are listed in the sections below.

EngineReference(s)
CRESTcrest-lab.org
GPU4PySCF10.1021/acs.jpca.4c05876
MOPAC10.21105/joss.08025
OpenMM10.1021/acs.jpcb.3c06662
PSI4psicode.org
PySCFpyscf.org
Quantum ESPRESSOquantum-espresso.org
TMDgithub.com/tmd-industries/tmd
xtbxtb-docs

Workflows

WorkflowReference(s)
ADME-ToxADMET-AI: 10.1093/bioinformatics/btae416
Binding affinityGnina: 10.1186/s13321-025-00973-x
AEV-PLIG: 10.1038/s42004-025-01428-y
Nesso-1: 10.64898/2026.08.01.742196
Conformer searchopenconf: github.com/rowansci/openconf
ETKDG: 10.1021/acs.jcim.5b00654
ETKDGv3: 10.1021/acs.jcim.0c00025
CREST: 10.1063/5.0197592
MCMM: github.com/ncasetti7/multiple_minimum_monte_carlo
DescriptorsMordred: 10.1186/s13321-018-0258-y
mordred-community: github.com/JacksonBurns/mordred-community
DockingGnina: 10.1186/s13321-025-00973-x
Vina: 10.1002/jcc.21334, 10.1021/acs.jcim.1c00203
Vinardo: 10.1371/journal.pone.0155183
QuickVina 2: 10.1093/bioinformatics/btv082
QuickVina-W: 10.1038/s41598-017-15571-7
Double-ended TS searchFSM: 10.1063/1.3664901
Internal-coordinate FSM: 10.1021/acs.jctc.5c01492
GSM: 10.1063/1.1691018
CI-NEB: 10.1063/1.1329672
DNEB: 10.1063/1.1636455
Geodesic interpolation: 10.1063/1.5090303
IDPP: 10.1063/1.4878664
Excited-state calculation (TDDFT)TDDFT: 10.1103/PhysRevLett.52.997
Tamm–Dancoff approximation: 10.1016/S0009-2614(99)01149-5
Electronic propertiesNatural transition orbitals: 10.1063/1.1558471
Free-energy perturbationOpenFF Sage citation guidance
OpenFF NAGL
Local resampling: 10.1021/acs.jctc.3c00539
REST background: 10.1073/pnas.0506346102
Fukui indicesCondensed indices (Yang and Mortier): 10.1021/ja00279a008
Global electrophilicity (GEI)10.1021/ja983494x
Hydrogen-bond acceptor/donor strength10.26434/chemrxiv-2025-kv6d6-v2
Interaction energy decompositionSAPT0 implementation: 10.1063/1.3426316, 10.1063/1.3656681
Method/basis performance: 10.1063/1.4867135
Intrinsic reaction coordinate (IRC)Predictor–corrector method: 10.1063/1.1724823
Hessian updating: 10.1021/ct0499783
Ion-mobility mass spectrometry predictionCoSIMS: 10.1021/acs.jpcb.9b01018
CoSIMS (Rowan's version): github.com/rowansci/cosims
LogPWildman–Crippen: 10.1021/ci990307l
Chemprop v2: 10.1021/acs.jcim.5c02332
SangsterLogP: 10.1038/s41597-026-07357-2
openCOSMO-RS: 10.1016/j.fluid.2024.114250
Macroscopic pKa and BBBUni-pKa: 10.1021/jacsau.4c00271
BBB physics-based precedent: 10.1021/acs.jcim.3c00150
Starling: 10.26434/chemrxiv-2025-t8s9z-v2
Kingfisher
Membrane permeabilityGNN-MTL: 10.1021/acsomega.5c04861
PyPermm
PerMM: 10.1021/acs.jcim.9b00225
Microscopic pKaFree-energy calibration: 10.1021/acs.jpca.1c03463
Rowan pKa: 10.26434/chemrxiv-2024-8489b
RDKit
Nevolianis 2025: 10.26434/chemrxiv-2025-8bj2t-v4
Multiple sequence alignment (MSA)ColabFold: 10.1038/s41592-022-01488-1
MMseqs2: 10.1038/nbt.3988
NMR predictionMagNET: 10.26434/chemrxiv.15005989/v1
Generalized Karplus equation: 10.1016/0040-4020(80)80155-4
Protein MD and pose-analysis MDOpenMM: 10.1021/acs.jpcb.3c06662
PhononsPhonopy citation guidance
Protein binder designBoltzGen
Protein preparationPROPKA 3: 10.1021/ct100578z, 10.1021/ct200133y
Hydride (optional protonation method): 10.1186/s13015-022-00215-x
Protein–ligand co-foldingBoltz-1: 10.1101/2024.11.19.624167
Boltz-2: 10.1101/2025.06.14.659707
Chai-1: 10.1101/2024.10.10.615955
OpenFold3 citation guidance
AlphaFold 3: 10.1038/s41586-024-07487-w
DeCAF: arXiv:2606.08375
Redox potential predictionReference shifts and benchmark: 10.1021/acs.jpca.0c05052
Electrode conversions: 10.1016/S0020-1693(99)00407-7
ScanWavefront propagation: 10.1063/5.0009232
Surface energySlab construction and reference cells: 10.1016/j.susc.2013.05.016
Solubilityfastsolv: 10.1038/s41467-025-62717-7
Kingfisher
ESOL: 10.1021/ci034243x
Rowan aqueous-model refits
CheMeleon: arXiv:2506.15792

Functionals/potentials

Functional/potentialPaper(s)
AIMNet210.26434/chemrxiv-2023-296ch
Egret-110.48550/arXiv.2504.20955
OMat24 eqV210.48550/arXiv.2410.12771
OMol25 eSEN10.48550/arXiv.2505.08762
Orb-v310.48550/arXiv.2504.06231
UMA10.48550/arXiv.2506.23971
GFN-FF10.1002/anie.202004239
GFN0-xTB10.26434/chemrxiv.8326202.v1
GFN1-xTB10.1021/acs.jctc.7b00118
GFN2-xTB10.1021/acs.jctc.8b01176
g-xTB10.26434/chemrxiv-2025-bjxvt
PM610.1007/s00894-007-0233-4
PM6-D3H4X10.1021/ct9000922
10.1016/j.cplett.2011.03.009
10.1021/ct200751e
PM6-ORG10.1007/s00894-023-05695-1
PM710.1007/s00894-012-1667-x
HF-3c10.1002/jcc.23317
B97-3c10.1063/1.5012601
B97-D3BJ10.1002/jcc.21759
r²SCAN-3c10.1063/5.0040021
ωB97X-3c10.1063/5.0133026
B3LYP10.1103/PhysRevA.38.3098
10.1103/PhysRevB.37.785
10.1139/p80-159
10.1021/j100096a001
M06-2X10.1007/s00214-007-0310-x
ωB97X-D310.1021/ct300715s
ωB97M-D3BJ10.1021/acs.jctc.8b00842
PBE10.1103/PhysRevLett.77.3865
PBE010.1063/1.478522
r²SCAN10.1021/acs.jpclett.0c02405
TPSS10.1103/PhysRevLett.91.146401
TPSSh10.1063/1.1626543
M06-L10.1063/1.2370993
M0610.1007/s00214-007-0310-x
CAM-B3LYP10.1016/j.cplett.2004.06.011
ωB97X-V10.1039/C3CP54374A
ωB97M-V10.1063/1.4952647
DSD-BLYP-D3BJ10.1021/jp1070852
Skala10.48550/arXiv.2506.14665
Hartree–Fock10.1017/S0305004100011919
10.1007/BF01340294
10.1103/PhysRev.34.1293

In addition to any functional/potential specific citations, please also cite LibXC for any DFT computations run.

Force fields

Cite the force field and version used in your workflow; protein, ligand, and water parameters may come from different models.

ModelReference(s)
AMBER ff14SB10.1021/acs.jctc.5b00255
AMBER ff19SB10.1021/acs.jctc.9b00591
AMBER ff99SB-ILDN10.1002/prot.22711
MMFF94sHalgren (1999)
OpenFF Sage and ToolkitOfficial version-specific citation guidance
TIP3P water10.1063/1.445869
TIP4P-Ew water10.1063/1.1683075
OPC water10.1021/jz501780a

Basis sets

For individual basis set references, see the Basis Set Exchange.

Pseudopotentials

LibraryReference(s)
SSSPPrandini et al.: 10.1038/s41524-018-0127-2
Per-element references: Materials Cloud SSSP tables
PseudoDojovan Setten et al.: 10.1016/j.cpc.2018.01.012
Full list of citations (PseudoDojo)

Solvent models

ModelReference(s)
ALPB10.1021/acs.jctc.1c00471
10.1063/1.2177251
CPCM10.1002/jcc.10189
COSMO10.1039/P29930000799
CPCM-X10.1021/acs.jpca.3c04382
COSMO-RSopenCOSMO-RS: 10.1016/j.fluid.2024.114250
GBn2 (protein MD MM/GBSA)10.1021/ct3010485
GBSA10.1021/acs.jctc.1c00471

Other

PurposeReference(s)
Crystal symmetryspglib: 10.1080/27660400.2024.2384822
High-symmetry band pathsHPKOT: 10.1016/j.commatsci.2016.10.015
Transition-state optimizationPartitioned rational-function optimization: 10.1021/j100247a015
Bofill Hessian updating: 10.1002/jcc.540150102
Molecular optimizationgeomeTRIC
Thermochemical correctionsCramer–Truhlar quasiharmonic treatment: 10.1021/jp205508z
Trajectory analysisMDTraj: 10.1016/j.bpj.2015.08.015
Structure handling (selected periodic engines)ASE
SMILES featuresRDKit
Dispersion correctionsD3: 10.1063/1.3382344
D3BJ: 10.1002/jcc.21759
D4 citation guidance
CM5 charges10.1021/ct200866d
Pose validationPoseBusters: 10.1039/D3SC04185A
PubChem importPubChem
RCSB import10.1093/nar/gkae1091

Contact us

If you notice we are missing any references to software or methods that are used at Rowan, please let us know at support@rowansci.com.