OMprotocolsio-protocol-repositorypradyumnasagar-open-research-skills#ors-metaResearchREST APIreproducibilitylab automationSearch and download published wet-lab protocols from protocols.io REST API. Find 90,000+ community protocols by keyword, DOI, or filter; extract steps, reagents, materials,...
OMqupath-pathologypradyumnasagar-open-research-skills#ors-metaResearchbioinformaticsdigital pathologymicroscopyUse QuPath 0.5.x for whole-slide image import, annotation, cell detection, pixel classification, deep-learning workflows (StarDist, Cellpose), and multiplexed analysis in digital...
OMscoping-reviewpradyumnasagar-open-research-skills#ors-metaResearchliterature reviewevidence synthesisscoping-reviewMap evidence landscapes in emerging fields using Arksey-O'Malley and JBI scoping review frameworks. Includes charting, narrative synthesis, consultation exercise, and gap...
OMsystematic-reviewpradyumnasagar-open-research-skills#ors-metaResearchprismasystematic reviewevidence synthesisConduct rigorous systematic reviews and meta-analyses following PRISMA 2020, including risk-of-bias assessment, heterogeneity analysis, publication bias evaluation, and evidence...
OMadmet-predictionpradyumnasagar-open-research-skills#ors-metaResearchcheminformaticsdrug discoveryqsar-modelingPredicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles,...
OMai-detection-awarenesspradyumnasagar-open-research-skills#ors-metaResearchresearch ethicsacademic-integrityai-detectionUse when you or your institution are using, evaluating, or responding to AI-detection tools (GPTZero, Turnitin, Copyleaks, Originality.ai, Pangram) — how detectors work, their...
OMai-disclosure-statementpradyumnasagar-open-research-skills#ors-metaResearchresearch-integrityacademic-publishingai-disclosureUse when drafting or auditing an AI/LLM disclosure statement for a manuscript, preprint, grant, or venue — what to include, where to put it, and how to meet major journal and...
OMai-disclosurepradyumnasagar-open-research-skills#ors-metaResearchresearch ethicsacademic-publishingai-disclosureUse when writing, reviewing, or editing the AI/LLM usage disclosure in a research manuscript, grant, or submission — covers venue-specific policies (Nature, Science, Cell, NEJM,...
OMconformer-generationpradyumnasagar-open-research-skills#ors-metaResearchcheminformaticsmolecular modelingcomputational chemistryGenerates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement,...
OMcovalent-designpradyumnasagar-open-research-skills#ors-metaResearchdrug designchemoinformaticscovalent-inhibitorsDesigns covalent inhibitors and warheads targeting cysteine (most common, ~98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit...
OMfree-energy-calculationspradyumnasagar-open-research-skills#ors-metaResearchdrug discoverycomputational chemistrychemoinformaticsPerforms alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd,...
OMgenerative-designpradyumnasagar-open-research-skills#ors-metaResearchdrug discoveryreinforcement learningchemoinformaticsDesigns novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol),...
OMimage-integritypradyumnasagar-open-research-skills#ors-metaResearchresearch-integrityimage-forensicswestern-blotUse when preparing, reviewing, or auditing research images (Western blots, gels, microscopy, EM, multi-panel figures) for submission — covers manipulation detection by proofreader...
OMirb-protocolpradyumnasagar-open-research-skills#ors-metaResearchregulatoryethics-complianceirbUse when writing, reviewing, or revising an Institutional Review Board (IRB) protocol for human-subjects research — anchors the protocol to the Belmont Report, the Common Rule (45...
OMmolecular-descriptorspradyumnasagar-open-research-skills#ors-metaResearchcheminformaticsdrug discoveryQSARCalculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA,...
OMmolecular-iopradyumnasagar-open-research-skills#ors-metaResearchfile parsingcheminformaticsrdkitReads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception,...
OMmolecular-standardizationpradyumnasagar-open-research-skills#ors-metaResearchcheminformaticsrdkitmolecular-standardizationStandardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer...
OMpharmacophore-modelingpradyumnasagar-open-research-skills#ors-metaResearchcheminformaticsdrug discoverymolecular modelingBuilds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow, Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation),...
OMpose-validationpradyumnasagar-open-research-skills#ors-metaResearchstructural biologyscientific computingchemoinformaticsValidates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle...
OMprotac-degraderspradyumnasagar-open-research-skills#ors-metaResearchcheminformaticsstructural biologymolecular modelingDesigns PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity),...