Index

a absolute metabolomics and thermodynamic analyses 272 acetyl-coenzyme A (acetyl-CoA) 268 additional reactions, draft to functional network biomass reactions 7 demand reactions 6 exchange reactions 6 non-growth associated ATP maintenance reactions 7 spontaneous reactions 7 transport reactions 6 AGORA 2 collection 61-62 AGORA collection 59-60 AI-agent for autonomous therapeutic peptide design 203-205 Akaike Information Criterion (AICc) 393 alcohol dehydrogenase (YqhD) 268 AllerCatPro 2.0 198 AllerTOP v.2 198 AlphaFold 111, 113, 114, 145, 170, 202, 307 alpha-ketoisovalerate decarboxylase (KivD) 268 amino acid auxotrophies 22 amino acid composition (AAC) 134-136, 194 AMPTrans-LSTM 201 ANNA16 232-234 anticancer peptide (ACP) 189, 195, 199 antifungal peptide (AFP) classification model 194 antimicrobial peptide classification models 192-193 anti-parasitic peptides (APPs) 195 antiviral peptide (AVP) classification model 193-194 artificial intelligence (AI) 63, 69, 75, 116, 131-153, 161-178, 187, 202-206, 220-222, 226-228, 236, 240-243, 253-260, 264, 273-274, 302, 333, 334, 341, 345, 354, 356 conventional computational approaches for predicting enzyme function 132-133 microbial cultivation process optimization 238-240 prediction of enzyme functions using deep learning 138-147 using machine learning 133-138 artificial intelligence (AI)-based metabolomics data processing and analysis 273-274 artificial intelligence (AI)/machine learning (ML) enabled retrobiosynthesis computer-aided synthesis planning 161 data standardization and model interpretability 177-178 enzyme prediction and design capabilities 176-177 enzyme selection and optimization 168-169 de novo enzyme design and discovery 172-174 enzyme catalytic efficiency 170-172 enzyme engineering 172 enzyme substrate specificity 169-170 integrating biocatalysis with chemocatalysis 175 Machine Learning and Big Data-enabled Biotechnology, First Edition.Edited by Hal S. Alper.