The Path to Synthetic Biology
Lowering the barriers to knowledge, making scientific exploration purer.
1. AI Search
12 items1.1 Overseas Models
5 items01ChatGPTFeaturedFeaturedOpenAI's most capable general-purpose model, ideal for scientific writing and logical reasoning.AI02GeminiGoogle's multimodal large model, excelling in long-text processing and literature analysis.Google03Google AI StudioDeveloper version of Gemini with free Pro model access and large context window.API04GrokModel launched by xAI with real-time Twitter feed integration.Twitter05PerplexityAI-powered search engine with real-time web access, providing accurate literature citations.Search
1.2 Domestic Models
5 items01DeepSeekFeaturedFeaturedDeepSeek, the shining star of Chinese open-source models with exceptional coding and mathematical capabilities.Domestic02Meta AI SearchAd-free AI search engine with structured search results display.Domestic03DoubaoByteDance's AI assistant with excellent voice interaction, ideal for daily Q&A.Domestic04KimiFrom Moonshot AI, supports ultra-long lossless context, excelling at reading long papers.Domestic05Tongyi QianwenAlibaba's AI model with strong comprehensive capabilities, suitable for business and document analysis.Domestic
1.3 Prompts
2 items01In-depth Research Paper AnalysisAct as a senior postdoc to comprehensively analyze literature figures, data, and mechanisms, generating a thesis-level report.Paper Reading02Structured Review Paper AnalysisDeconstruct complex review articles into well-structured, informative Chinese academic reports for rapid domain mastery.Review
2. Academic Search
15 items2.1 Academic Search (Foreign Literature)
7 items01Google ScholarFeaturedFeaturedWorld's largest academic literature index database, essential for research.Literature02PubMedFeaturedFeaturedNIH-maintained biomedical literature database, the most authoritative search platform in life sciences.Biomedical03X-MolFeaturedFeaturedComprehensive academic platform providing literature news, academic community, and research tools.Academic04Web of ScienceWorld's most authoritative academic citation database, essential for research evaluation and literature review.Citation05Semantic ScholarAI-powered free academic search engine with accurate one-sentence summaries (TLDR) and citation intent analysis.AI06Bing AcademicMicrosoft Bing's academic search with clean interface and wide resource coverage.Search07ProQuestLeading global academic database platform covering journal articles, dissertations (PQDT), and e-books across humanities, social sciences, biomedicine and more.Dissertation
2.2 Academic Search (Chinese Literature)
4 items01CNKIFeaturedFeaturedChina's largest Chinese academic literature database, essential for finding theses and dissertations.Chinese02Wanfang DataComprehensive Chinese academic resource database covering journals, patents, and standards.Chinese03Baidu ScholarAggregates massive Chinese and English literature, providing free plagiarism checking.Aggregation04PubScholarChinese Academy of Sciences' public welfare platform, providing free access to 80 million full-text articles with iFlytek translation.Free
2.3 Journal Rankings & Partitions
1 items2.4 AI Literature Analysis & Network Maps
3 items01SciSpaceThe ultimate PDF reader with AI Copilot for word translation, figure/formula explanation, and core conclusion summarization.PDF Reading02Connected PapersExcellent literature topology network visualization tool. Input one paper to instantly map the field's context.Literature Topology03ElicitYour AI postdoc assistant that automatically extracts experimental data, methods, and results from vast literature into tables.Data Extraction
3. Literature Download
10 items3.1 Direct Download
6 items01Sci-hub (Recommended)FeaturedFeaturedBreaking academic barriers, free download of most paid papers worldwide.Free02SciWork (Recommended)FeaturedFeaturedLiterature mutual aid platform solving difficult paper downloads through community power.Mutual Aid03GeenMedicalChinese literature download platform with massive literature resource search and download.Download04ScidownAcademic resource download navigation without VPN needed.Navigation05Longmao AcademicAcademic navigation site aggregating multiple Google Scholar mirrors and download portals.Navigation06Wenxian TribeProvides literature download plus e-books and patent search.E-book
3.2 Literature Management & Reading
4 items01Zotero (Recommended)FeaturedFeaturedFree open-source literature management tool with rich plugins, dramatically improving research efficiency.Literature Management02EndNoteWorld's most classic literature management tool, essential paper writing assistant for researchers.Literature Management03Xiao Lv JingProfessional SCI literature reader with full-text translation, note management, and literature analysis.Literature Reading04ScholareadAI-driven literature reading and management platform providing summary, translation, and analysis.Literature Reading
4. Patents
6 items4.1 Patent Search
3 items4.2 Patent Download
3 items5. Natural Products
23 items5.1 Spectral Analysis & Structure Elucidation
8 items01Weipu DataFeaturedFeaturedWell-known NMR carbon spectrum database in China.NMR02GNPSFeaturedFeaturedGlobal Natural Products Social molecular networking, the ultimate mass spectrometry data analysis tool.Mass Spectrometry03NP-MRDNatural product magnetic resonance database for structure elucidation.NMR04SIRIUSTop AI mass spectrometry tool integrating CSI:FingerID to directly predict metabolite structures from high-res MS/MS data.Mass Spectrometry05SMARTNMR-based rapid natural product structure deduplication and identification tool.NMR06DeepSATDeep learning-assisted spectrum analysis tool.AI07DP5Probabilistic prediction tool for NMR structure elucidation.NMR08Pep2PathLinks peptide mass spectrometry data to genomic biosynthetic gene clusters.Peptide
5.2 Specialized Natural Product Libraries
6 items01CMNPDComprehensive marine natural product database, authoritative platform for discovering novel marine scaffolds and highly active molecules.Marine02TCMSPTraditional Chinese Medicine systems pharmacology database containing massive TCM active ingredients and target information.TCM03KNApSAcKClassic species-metabolite relationship database for precise queries of natural products in specific plants or microorganisms.Plant04NPEdiaEncyclopedia focused on natural products and their biological activities.Encyclopedia05NP AtlasMicrobial natural product atlas providing structure and source information.Microbe06DBAASPAntimicrobial peptide structure and activity database.Antimicrobial Peptide
5.3 Comprehensive Chemical Databases
5 items01PubChemFeaturedFeaturedWorld's largest chemical molecule database provided by NIH.NIH02SciFinderFeaturedFeaturedAuthoritative chemistry research platform by CAS, covering 275M+ substances, 150M+ reactions, and 59M+ references.CAS03ChemSpiderFree chemical structure database provided by Royal Society of Chemistry.RSC04MoNAMass Spectrometry library, one of the largest free untargeted metabolomics and natural product MS databases.Mass Spectrometry05ChEBIDatabase of chemical entities of biological interest.EBI
5.4 Property Prediction & Computational Tools
4 items01SwissADMEExtremely intuitive drug-likeness, water solubility, brain penetration, and ADME prediction tool, preferred for research.ADME02SwissTargetPredictionPredicts unknown target proteins of small molecule natural products in humans based on reverse pharmacophore matching.Target Prediction03ADMETlab 3.0Comprehensive evaluation of drug absorption, distribution, metabolism, excretion, and toxicity.Drug Design04ChemCalcChemical calculator for rapid molecular formula and isotope distribution calculation.Tool
6. Gene Tools
36 items6.1 Comprehensive Gene Sequence Analysis
13 items01NCBIFeaturedFeaturedNational Center for Biotechnology Information, core gateway for life sciences.Authoritative02AugustusFeaturedFeaturedEukaryotic gene and intron annotation prediction tool.Gene Prediction03NeurosnapAI-based comprehensive biological analysis platform.AI04EBI ToolsCollection of bioinformatics online tools provided by EBI.EBI05National Genomics Data CenterChina's National Genomics Data Center providing massive genomic data resources.China06EnsemblExtremely powerful eukaryotic genome browser and annotation database, preferred for transcript lookup.Genome07TBtoolPowerful batch processing and analysis tool for biological sequences.Software08GTEx PortalGene tissue expression database for studying gene expression patterns across different tissues.Gene Expression09GeneCardsComprehensive human gene database integrating gene function, expression, variation and more.Human Gene10IMPIntegrated medicinal plant omics platform with 1,007 high-quality plant genomes, 800M+ genes, and 2,158 transcriptomic samples.Plant11SGDSaccharomyces cerevisiae genome database providing detailed yeast gene sequence, annotation, function, and protein information.Yeast12NicomicsTobacco genome database developed by Huazhong Agricultural University providing tobacco genome and transcriptomics data.Tobacco13DOE JGIUS Department of Energy Joint Genome Institute providing microbial genome databases like IMG, GOLD, Genome Portal and BBTools.Genome
6.2 Domain & Homology Analysis
5 items01InterProFeaturedFeaturedDatabase of protein families, domains, and functional sites.Domain02HMMERFeaturedFeaturedSequence homology search tool based on hidden Markov models.Homology03CD SearchFeaturedFeaturedNCBI conserved domain database search.NCBI04eggNOG-MapperFast gene functional annotation tool based on eggNOG database supporting GO, KEGG, COG annotations, 2-15x faster than BLAST.Functional Annotation05SCOP2Protein structure classification database.Structure
6.3 Sequence Alignment & Phylogenetic Trees
5 items01Clustal OmegaFeaturedFeaturedFast and accurate multiple sequence alignment tool.Alignment02MEGAFeaturedFeaturedMolecular evolutionary genetics analysis software, essential for phylogenetic tree construction.Phylogenetic Tree03MAFFTHigh-performance multiple sequence alignment program.Alignment04JalviewSoftware for editing, visualizing, and analyzing multiple sequence alignments.Visualization05iTOLOnline phylogenetic tree visualization and annotation tool.Phylogenetic Tree
6.4 Genome & Primer Design
3 items6.5 Gene Editing & CRISPR
5 items01CHOPCHOPFeaturedFeaturedHarvard-developed easy-to-use CRISPR/Cas (Cas9, Cpf1, etc.) sgRNA design and off-target prediction tool.CRISPR02CRISPOROne of the most cited 'gold standard' tools, evaluating off-target effects and outputting primer sequences for cloning.Gold Standard03Benchling CRISPRMost popular comprehensive plasmid and sequence design platform in industry with powerful CRISPR gRNA design module.Comprehensive Platform04Cas-OFFinderUltra-fast search for CRISPR/Cas off-target sites with customizable mismatches and bulges.Off-target Analysis05Synthego DesignFree online design tool from leading CRISPR company, especially good for multi-gene knockout experiments.Free Commercial
6.6 Plasmid & Clone Construction
2 items6.7 Expression Elements & RNA Analysis
3 items01RBS CalculatorSynthetic biology core tool from Salis Lab for precise prediction and design of ribosome binding sites (RBS) to control translation rates.RBS02BPROMClassic bacterial promoter prediction tool for finding transcription start sites and -10/-35 regions.Promoter03RNAfoldStandard tool for predicting RNA secondary structure, essential for riboswitch design or mRNA stability optimization.RNA
7. Protein Tools
70 items7.1 Comprehensive Protein Analysis Platforms
5 items01NovoproFeaturedFeaturedPeptide and protein online tools from Novopro.Toolkit02TamarindAI-based protein structure and function analysis platform.AI03ExpasyProteomics server provided by Swiss Institute of Bioinformatics.Proteomics04DTU Health TechBioinformatics toolkit from Technical University of Denmark.Membrane Protein05CD-HITEfficient protein sequence clustering tool.Sequence Clustering
7.2 Protein Structure Prediction
14 items01Swiss-ModelFeaturedFeaturedFully automated protein homology modeling server.Homology Modeling02ProtenixFeaturedFeaturedProfessional protein analysis and structure prediction server.Analysis03AlphaFold 3Google DeepMind's latest generation protein structure prediction model.Structure Prediction04ColabFoldRun AlphaFold2 in browser without local computing power.Structure Prediction05Chai-1Cutting-edge molecular structure prediction model with top accuracy.AI06RoseTTAFoldProtein structure prediction tool from Baker Lab.Structure Prediction07ESMFoldMeta's language model-based fast protein structure prediction.Meta08I-TASSERIterative thread assembly algorithm, classic structure prediction tool.Structure Prediction09QUARKAb initio protein structure prediction tool.Ab initio10RobettaBaker Lab's protein structure prediction server.Structure Prediction11AWSEMAtomic movability-based protein structure prediction tool.Structure Prediction12DSSPProtein secondary structure prediction and classification.Secondary Structure13Dali ServerWeb server for protein structure alignment.Structure Alignment143D-Beacons NetworkNetwork platform integrating multiple structure prediction services.Structure Prediction
7.3 Molecular Docking
12 items01AutoDock VinaFeaturedFeaturedFaster and more accurate open-source docking engine.Docking02AutoDockStandard software in molecular simulation and docking.Docking03HDockHybrid algorithm protein-protein/docking server.Docking04DiffDockDiffusion model-based molecular docking tool.AI05ClusProProtein-protein docking server from Boston University.Protein Docking06CABS-dockPeptide-protein docking tool from University of Warsaw.Peptide Docking07HPEPDOCKPeptide-protein docking server from HUST.Peptide Docking08Flexible Peptide DockingFlexible peptide docking server from Meiler Lab.Flexible Docking09RPBSBiomolecular simulation portal from Paris Diderot.Molecular Simulation10CavityPlusProtein cavity detection tool from Peking University.Cavity Detection11ChemSARCompound SAR analysis and docking tool.SAR12DeepScreeningDeep learning-based virtual screening tool.Virtual Screening
7.4 Protein Sequence & Structure Databases
8 items01UniProtFeaturedFeaturedUniversal protein resource with sequence and function info.Database02RCSB PDBFeaturedFeaturedProtein Data Bank with experimental structures.Crystal03NCBI ProteinProtein sequence database from NCBI.NCBI04AlphaFold DBDatabase of protein structures predicted by AlphaFold.Database05STRINGWorld's largest PPI network database.PPI06IntActMolecular interaction database from EBI.Protein Interaction07The Human Protein AtlasHuman protein atlas with expression data.Human Protein08OPMMembrane protein orientation database.Membrane Protein
7.5 Enzyme Properties & Localization Prediction
8 items01SignalPFeaturedFeaturedPredicts signal peptides and cleavage sites.Signal Peptide02DeepTMHMMFeaturedFeaturedDeep learning transmembrane prediction.Transmembrane03ExpOptimizerCodon optimization for heterologous expression.Expression04Protein-SolPredicts protein solubility.Solubility05Rare Codon AnalyzerAnalyzes rare codons.Codon06PPSPPhosphorylation site prediction.Phosphorylation07GPS-SUMOSUMOylation site prediction.SUMOylation08MAI-TargetFisherMulti-scale target prediction.Target Prediction
7.6 Enzyme Mining & Functional Annotation
5 items7.7 Protein Design & Engineering
11 items01FoldXFeaturedFeaturedMutation stability effect.Stability02SaProtFeaturedFeaturedStructure-aware protein LM from Westlake.Language Model03RFdiffusionDiffusion model protein generation from Baker Lab.Diffusion Model04ODesignDeep learning affinity optimization.Affinity05BindCraftDL protein-ligand binding design.Ligand Binding06CACLENSAI protein optimization.AI07CATNIPML binding affinity prediction.Binding Prediction08EZSpecificityEnzyme specificity optimization.Enzyme Specificity09MPEKProtease stability prediction.Protease10LigandMPNNProteinMPNN with ligand support.Sequence Design11ProteinMPNNDL sequence design from structure.Sequence Design
7.8 3D Structure Visualization
7 items01PyMOLFeaturedFeaturedClassic protein visualization software.Visualization02UCSF ChimeraXFeaturedFeaturedNext-gen molecular visualization.Visualization03Mol*Smooth web 3D visualization.3D043Dmol.jsLightweight WebGL visualization.WebGL05ESPriptAlignment figure tool.Sequence Alignment06WebLogoSequence LOGO tool.Sequence LOGO07colornamesChimera color documentation.Visualization
8. Biosynthesis & Metabolism
32 items8.1 BGC Mining & Network Analysis
13 items01antiSMASHFeaturedFeaturedMost authoritative secondary metabolite BGC mining and analysis tool.Mining02BiG-SCAPEFeaturedFeaturedCalculates gene cluster similarity and builds GCF networks.BGC03FunBGCsFeaturedFeaturedFungal BGC functional analysis tool.Fungi042ndFindFeaturedFeaturedSecondary metabolite biosynthesis gene finder.Search05DeepSeMSAI-accelerated natural product discovery, biosynthetic pathway identification and chemical structure analysis web server.AI06DeepBGCDeep learning BGC mining tool for discovering novel 'dark matter' gene clusters.AI07ARTSAntibiotic resistance target search for new antibiotic discovery.Antibiotic08SMBPSecondary metabolite biosynthesis mining platform.BGC09FunGeneClusterSFungal secondary metabolite BGC mining tool.Fungi10FunARTSFungal antibiotic resistance target search.Fungi11BAGEL4Tool for mining bacteriocins and RiPPs.Bacteriocin12RiPPMinerRiPP automatic mining and analysis.RiPPs13GenoCGLLMPlant BGC analysis platform.Gene Cluster
8.2 Domain & Substrate Prediction
9 items01CAGECATFeaturedFeaturedWeb toolbox for rapid homologous gene cluster search and comparative visualisation of genomic loci, including BGCs and genomic islands.BGC02DeepAdenFeaturedFeaturedDeep learning NRPS adenylation domain prediction.NRPS03PKS/NRPS AnalysisClassic PKS and NRPS domain analysis.PKS04NaPDoS2Phylogeny-based secondary metabolite domain detection.Classification05NRPSpredictor2Predicts NRPS adenylation domain substrate specificity.NRPS06SBSPKSPKS structure and sequence analysis.PKS07LassoPredLasso peptide domain prediction.Lasso08PARASPKS/NRPS adenylation domain substrate prediction.NRPS09NRPSTransformerNRPS/PKS analysis and product prediction.NRPS
8.3 Metabolic Pathway Design & Retrosynthesis
4 items01KEGGKyoto Encyclopedia of Genes and Genomes, authoritative pathway analysis database.Metabolic Pathway02RetroBioCatPowerful biocatalysis and computer-aided retrosynthesis platform.Retrosynthesis03BioCycCurated metabolic pathway database with detailed species-specific models.Metabolic Network04SelenzymeAutomated enzyme matching and screening for metabolic pathways.Enzyme Screening
8.4 BGC & Metabolic Model Databases
6 items01MIBiGFeaturedFeaturedStandard BGC database with known functions.Database02antiSMASH DatabaseantiSMASH predicted BGC database.BGC03DoBISCUITPKS/NRPS BGC database from Japanese NITE.PKS04IMG-ABCBGC atlas from JGI.JGI05BiGG ModelsLargest genome-scale metabolic model database.GEMs06NP Discovery CenterNatural products discovery center database.Natural Product
9. Biomedicine
9 items9.1 Drug Databases
5 items01DrugBankMost authoritative drug target and interaction database.Drug02ChEMBLBioactive molecule database from EBI.Drug03BindingDBProtein-ligand binding affinity database.Binding Affinity04IUPHARIUPHAR drug target and receptor database.Pharmacology05ClinPGxClinical pharmacogenomics database.Clinical
9.2 Cancer Omics Analysis
4 items10. Lab Supplies & Reagents
10 items10.1 Chemical Reagents & Consumables
7 items01ChemicalBookChemical information search platform.Chemistry02AladdinComprehensive chemical supplier.Reagent03MacklinDomestic chemical platform.Reagent04SinopharmSinopharm reagents.Reagent05SolarbioDomestic bio reagent brand.Reagent06Sigma-AldrichLeading global reagent supplier.Reagent07Thermo FisherWorld's largest scientific provider.Reagent