Ahmad S, Chitkara P, Khan FN, Kishan A, Alok V, Ramlal A, Mehta S (2021) Mobile Technology Solution for COVID-19: Surveillance and Prevention. In: Raza K (ed) Computational intelligence methods in COVID-19: surveillance, prevention, prediction and diagnosis. Studies in computational intelligence, vol 923. Springer, Singapore
Google Scholar
Armenteros JJA, Salvatore M, Emanuelsson O, Winther O, Von Heijne G, Elofsson A, Nielsen H (2019) Detecting sequence signals in targeting peptides using deep learning, vol 5. Life Sci Allian, Woodbury
Google Scholar
Bailey TL, Johnson J, Grant CE, Noble WS (2015) The MEME suite. Nuc Acid Res 43(W1):W39–W49
Article
CAS
Google Scholar
Bains A, Chawla P, Kaur S, Najda A, Fogarasi M, Fogarasi S (2021) Bioactives from mushroom: health attributes and food industry applications. Materials 14(24):7640
Article
CAS
Google Scholar
Berlanas C, Ojeda S, López-Manzanares B, Andrés-Sodupe M, Bujanda R, del Pilar Martínez-Diz M, Diaz-Losada E, Gramaje D (2020) Occurrence and diversity of black-foot disease fungi in symptomless grapevine nursery stock in Spain. Plant Dis 104(1):94–104
Article
CAS
Google Scholar
Boddy L (2016) Interactions with humans and other animals. In: Watkinson SC, Boddy L, Money NP (eds) The fungi. Academic Press, Cambridge, pp 293–336
Chapter
Google Scholar
Cai J, Li X, Du H, Jiang C, Xu S, Cao Y (2020) Immunomodulatory significance of natural peptides in mammalians: promising agents for medical application. Immunobiology 225(3):151936
Article
CAS
Google Scholar
Chalamaiah M, Yu W, Wu J (2018) Immunomodulatory and anticancer protein hydrolysates (peptides) from food proteins: a review. Food Chem 245:205–222
Article
CAS
Google Scholar
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genom Res 14(6):1188–1190
Article
CAS
Google Scholar
Deleage G, Tinland B, Roux B (1987) A computerised version of Chou and Fasman method for predicting the secondary structure of proteins. Anal Biochem 163:292–297
Article
CAS
Google Scholar
Desta IT, Porter KA, Xia B, Kozakov D, Vajda S (2020) Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure 28(9):1071–1081
Article
CAS
Google Scholar
Duhovny D, Nussinov R, Wolfson HJ (2002) Efficient Unbound Docking of Rigid Molecules. In: Guigo R, Gusfield D (eds) Proceedings of the 2’nd Workshop on algorithms in bioinformatics (WABI) Rome, Italy. Lecture Notes in Computer Science, vol 2452. Springer Verlag, pp 185–200
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
Article
CAS
Google Scholar
Ejike UC, Chan CJ, Okechukwu PN, Lim RLH (2020) New advances and potentials of fungal immunomodulatory proteins for therapeutic purposes. Crit Rev Biotechnol 40(8):1172–1190
Article
CAS
Google Scholar
Faure G, Joseph AP, Craveur P, Narwani TJ, Srinivasan N, Gelly JC, Rebehmed J, de Brevern AG (2019) iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach. Source Code Biol Med 14(1):1–5
Article
Google Scholar
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol 39:783–791
Google Scholar
Garcia-Lora A, Algarra I, Garrido F (2003) MHC class I antigens, immune surveillance, and tumor immune escape. J Cell Physiol 195(3):346–355
Article
CAS
Google Scholar
Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi chuan = Hereditas 29(8):1023–1026
Article
CAS
Google Scholar
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, London, Information Retrieval Ltd., c1979-c2000. Oxford University Press, UK, 41(41), pp 95–98
Hallgren J, Tsirigos KD, Pedersen MD, Armenteros JJA, Marcatili P, Nielsen H, Krogh A, Winther O (2022) DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv. https://doi.org/10.1101/2022.04.08.487609
Article
Google Scholar
Hesami AA, Zakery-Asl MA, Gardonpar H (2014) The effect of three amino acids (asparagine, glutamine and glycine) on some quantity and quality characteristics of white button mushroom (Agaricus bisporus). Intl J Farm Alli Sci 3(2):187–191
Google Scholar
Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585–W587
Article
Google Scholar
Hsu HC, Hsu CI, Lin RH, Kao CL, Lin JY (1997) Fip-vvo, a new fungal immunomodulatory protein isolated from Volvariella volvacea. Biochem J 323(2):557–565
Article
CAS
Google Scholar
Hyde KD, Al-Hatmi A, Andersen B, Boekhout T, Buzina W, Dawson TL Jr, Eastwood DC, Jones EBG, de Hoog S, Kang Y, Longcore JE, McKenzie EHC, Meis JF, Pinson-Gadais L, Rathnayaka AR, Richard-Forget F, Stadler M, Theelen B, Thongbai B, Tsui CK (2018) The world’s ten most feared fungi. Fungal Divers 93(1):161–194
Article
Google Scholar
Jiang FY, Li H, Yin LL, Ma J, Wang HF (2016) Cloning and bioinformatics of fungal lmmunomodulatory protein gene from Ganoderma amboinense. J Qiongzhou Univ 23(2):54–59
Google Scholar
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8(3):275–282
Article
CAS
Google Scholar
Kakoti M, Dullah S, Hazarika DJ, Barooah M, Boro RC (2022) Cinnabarinic acid from Trametes coccinea fruiting bodies exhibits antibacterial activity through inhibiting the biofilm formation. Arch Microbiol 204(3):1–10
Article
Google Scholar
Khan FN, Khanam AA, Ramlal A, Ahmad S (2021) A review on predictive systems and data models for COVID-19. In: Raza K (ed) Computational intelligence methods in COVID-19: surveillance, prevention, prediction and diagnosis. Studies in computational intelligence, vol 923. Springer, Singapore
Google Scholar
Khatun S, Islam A, Cakilcioglu U, Chatterjee NC (2012) Research on mushroom as a potential source of nutraceuticals: a review on indian perspective. J Exp Agric Int 2(1):47–73
Google Scholar
Khavinson V, Linkova N, Dyatlova A, Kuznik B, Umnov R (2020) Peptides: prospects for Use in the treatment of COVID-19. Molecules 25(19):4389
Article
CAS
Google Scholar
Kino K, Yamashita A, Yamaoka K, Watanabe J, Tanaka S, Ko K, Shimizu K, Tsunoo H (1989) Isolation and characterization of a new immunomodulatory protein, ling zhi-8 (LZ-8), from Ganoderma lucidium. J Biol Chem 264(1):472–478
Article
CAS
Google Scholar
Kishino H, Hasegawa M (2001) Maximum likelihood. In: Brenner S, Miller JH (eds) Encyclopedia of genetics. Academic Press, Cambridge, pp 1157–1160
Chapter
Google Scholar
Ko JL, Hsu CI, Lin RH, Kao CL, Lin JY (1995) A new fungal immunomodulatory protein, FIP-fve isolated from the edible mushroom, Flammulina velutipes and its complete amino acid sequence. Eur J Biochem 228(2):244–249
Article
CAS
Google Scholar
Kowalczyk JE, Peng M, Pawlowski M, Lipzen A, Ng V, Singan V, Wang M, Grigoriev IV, Mäkelä MR (2019) The white-rot basidiomycete Dichomitus squalens shows highly specific transcriptional response to lignocellulose-related aromatic compounds. Front Bioeng Biotechnol 7:229
Article
Google Scholar
Kozakov D, Beglov D, Bohnuud T, Mottarella S, Xia B, Hall DR, Vajda S (2013) How good is automated protein docking? Proteins. Struct Funct Bioinform 81(12):2159–2166
Article
CAS
Google Scholar
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S (2017) The ClusPro web server for protein-protein docking. Nat Protoc 12(2):255–278
Article
CAS
Google Scholar
Kumar TA (2013) CFSSP: Chou and Fasman secondary structure prediction server. Wide Spectrum: Res J 1(9):15–19
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Bio Evol 35:1547–1549
Article
CAS
Google Scholar
Letunic I, Khedkar S, Bork P (2021) SMART: recent updates, new developments and status in 2020. Nuc Acid Res 49(D1):D458–D460
Article
CAS
Google Scholar
Li QZ, Wang XF, Zhou XW (2011) Recent status and prospects of the fungal immunomodulatory protein family. Crit Rev Biotechnol 31(4):365–375
Article
Google Scholar
Li SY, Shi LJ, Ding Y, Nie Y, Tang XM (2015) Identification and functional characterization of a novel fungal immunomodulatory protein from Postia placenta. Food Chem Toxicol 78:64–70
Article
CAS
Google Scholar
Li S, Zhao L, Xu W, Jiang Z, Kang J, Wang F, Xin F (2016) Identification and characterisation of a novel protein FIP-sch3 from Stachybotrys chartarum. PLoS ONE 1(12):e0168436
Article
Google Scholar
Li S, Jiang Z, Xu W, Xie Y, Zhao L, Tang X, Wang F, Xin F (2017) FIP-sch2, a new fungal immunomodulatory protein from Stachybotrys chlorohalonata, suppresses proliferation and migration in lung cancer cells. Appl Microbiol Biotechnol 101(8):3227–3235
Article
CAS
Google Scholar
Li QZ, Zheng YZ, Zhou XW (2019) Fungal immunomodulatory proteins: characteristic, potential antitumor activities and their molecular mechanisms. Drug Discov Today 24(1):307–314
Article
CAS
Google Scholar
Li JP, Lee YP, Ma JC, Liu BR, Hsieh NT, Chen DC, Chu CL, You RI (2021) The enhancing effect of fungal immunomodulatory protein-volvariella volvacea (FIP-vvo) on maturation and function of mouse dendritic cells. Life 11(6):471
Article
CAS
Google Scholar
Li SY, Hou LZ, Gao YX, Zhang NN, Fan B, Wang F (2022) FIP-nha, a fungal immunomodulatory protein from Nectria haematococca, induces apoptosis and autophagy in human gastric cancer cells via blocking the EGFR-mediated STAT3/Akt signaling pathway. Food Chemistry: Mol Sci 4:100091
CAS
Google Scholar
Lin WH, Hung CH, Hsu CI, Lin JY (1997) Dimerization of the N-terminal amphipathic α-helix domain of the fungal immunomodulatory protein from Ganoderma tsugae (Fip-gts) defined by a yeast two-hybrid system and site-directed mutagenesis. J Biol Chem 272(32):20044–20048
Article
CAS
Google Scholar
Lin JW, Hao LX, Xu GX, Sun F, Gao F, Zhang R, Liu LX (2009) Molecular cloning and recombinant expression of a gene encoding a fungal immunomodulatory protein from Ganoderma lucidum in Pichia pastoris. World J Microbiol Biotechnol 25(3):383–390
Article
CAS
Google Scholar
Lin TY, Hua WJ, Yeh H, Tseng AJ (2021) Functional proteomic analysis reveals that fungal immunomodulatory protein reduced expressions of heat shock proteins correlates to apoptosis in lung cancer cells. Phytomedicine 80:153384
Article
CAS
Google Scholar
Lin J, Chen H, Bai Y, Li S, Liang G, Fan T, Gao N, Wu X, Li H, Chen G, Gao Y, Fan J (2022) Ganoderma immunomodulatory proteins: mushrooming functional FIPs. Applied Microbiol Biotechnol. https://doi.org/10.1007/s00253-022-11839-9
Article
Google Scholar
Liu Y, Bastiaan-Net S, Wichers HJ (2020) Current understanding of the structure and function of fungal immunomodulatory proteins. Front Nutr 7:132
Article
CAS
Google Scholar
Mallikarjuna SE, Ranjini A, Haware DJ, Vijayalakshmi MR, Shashirekha MN, Rajarathnam S (2013) Mineral composition of four edible mushrooms. J Chem. https://doi.org/10.1155/2013/805284
Article
Google Scholar
Mbuge DO, Mutai EBK (2018) Influence of heat treatment on vitamin C levels in Oyster Mushroom. IJRTEM 47–52
Naeem MY, Ozgen S, Sumayya R (2020) Emerging role of edible mushrooms in food industry and its nutritional and medicinal consequences. Eurasian J Food Sci Technol 4(1):6–23
Google Scholar
Ott M (2010) Inference of large phylogenetic trees on parallel architectures. Doctoral dissertation, Technische Universität München
Pavlicevic M, Marmiroli N, Maestri E (2022) Immunomodulatory peptides—A promising source for novel functional food production and drug discovery. Peptides 148:170696
Article
CAS
Google Scholar
Pevsner J (2009) Bioinformatics and functional genomics, 2nd edn. John Wiley & Sons, New Jersey
Book
Google Scholar
Phillips R (2005) Mushrooms and other fungi of North America, vol 2. Firefly Books, Buffalo
Google Scholar
Qu ZW, Zhou SY, Guan SX, Gao R, Duan ZW, Zhang X, Sun WY, Fan WL, Chen SS, Chen LJ, Lin JW, Ruan YY (2018) Recombinant expression and bioactivity comparison of four typical fungal immunomodulatory proteins from three main Ganoderma Species. BMC Biotechnol 18(1):1–12
Article
CAS
Google Scholar
Rahi DK, Malik D (2016) Diversity of mushrooms and their metabolites of nutraceutical and therapeutic significance. J Mycol. https://doi.org/10.1155/2016/7654123
Article
Google Scholar
Ramlal A, Ahmad S, Kumar L, Khan FN, Chongtham R (2021) From molecules to patients: the clinical applications of biological databases and electronic health records. In: Raza K, Dey N (eds) Translational Bioinformatics in Healthcare and Medicine. Elsevier, Netherlands, pp 107–125
Chapter
Google Scholar
Rampersad SN (2020) Pathogenomics and management of Fusarium diseases in plants. Pathogens 9(5):340
Article
CAS
Google Scholar
Rehman I, Farooq M, Botelho S (2019) Biochemistry, Secondary Protein Structure. NCBI Bookshelf.https://www.ncbi.nlm.nih.gov/books/NBK470235/
Rigsby RE, Parker AB (2016) Using the PyMOL application to reinforce visual understanding of protein structure. Biochem Mol Biol Educ 44(5):433–437
Article
CAS
Google Scholar
Sarma TC, Sarma I, Patiri BN (2010) Wild edible mushrooms used by some ethnic tribes of western Assam. The Bioscan 3:613–625
Google Scholar
Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33(suppl2):W363–W367
Article
CAS
Google Scholar
Semeiks J, Borek D, Otwinowski Z, Grishin NV (2014) Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys. BMC Genom 15(1):1–16
Article
Google Scholar
Singh S, Singh A (2014) Status and scope of mushroom cultivation in Haryana constraints and future outlook. In: Proceedings of the 8th International Conference on Mushroom Biology and Mushroom Products (ICMBMP8). p 612
Sharma N, Naorem LD, Jain S, Raghava GP (2022) ToxinPred2: an improved method for predicting toxicity of proteins. Brief Bioinform. https://doi.org/10.1093/bib/bbac174
Article
Google Scholar
Sun FF, Sun SL, Tian J, Duan CX, Zhu ZD (2021) First report of Paramyrothecium foliicola causing leaf spot on Vigna radiata in China. Plant Dis 105(4):1207
Article
Google Scholar
Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D (2017) New additions to the ClusPro server motivated by CAPRI. Proteins Struct Funct Bioinform 85(3):435–444
Article
CAS
Google Scholar
Valverde ME, Hernández-Pérez T, Paredes-López O (2015) Edible mushrooms: improving human health and promoting quality life. Int J Microbiol. https://doi.org/10.1155/2015/376387
Article
Google Scholar
Vashishta BR, Sinha AK, Kumar A (2007) Botany for Degree students: fungi. S. Chand Publishing, New Delhi
Google Scholar
Wang XF, Su KQ, Bao TW, Cong WR, Chen YF, Li QZ, Zhou XW (2012) Immunomodulatory effects of fungal proteins. Curr Top Nutraceutical Res 10(1):1–12
Google Scholar
Wu MY, Hsu MF, Huang CS, Fu HY, Huang CT, Yang CS (2007) A 2.0 Å structure of GMI, a member of the fungal immunomodulatory protein family from Ganoderma microsporum. Protein crystallogr 2:132
Google Scholar
Xu H, Kong YY, Chen X, Guo MY, Bai XH, Lu YJ, Li W, Zhou XW (2016) Recombinant FIP-gat, a fungal immunomodulatory protein from Ganoderma atrum, induces growth inhibition and cell death in breast cancer cells. J Agricult Food Chem 64(13):2690–2698
Article
CAS
Google Scholar
Yang Z, Nielsen R, Hasegawa M (1998) Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Bio Evol 15(12):1600–1611
Article
CAS
Google Scholar
Yang Y, Huang P, Ma Y, Jiang R, Jiang C, Wang G (2022) Insights into intracellular signaling network in Fusarium species. Int J Biol Macromol 222(A):1007–1014
Article
CAS
Google Scholar
Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins: Struct Funct Bioinform 64(3):643–651
Article
CAS
Google Scholar
Xu X, Yan H, Chen J, Zhang X (2011) Bioactive proteins from mushrooms. Biotechnol Adv 29(6):667–674
Article
CAS
Google Scholar
Zhang C, Vasmatzis G, Cornette JL, DeLisi C (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Bol 267(3):707–726
Article
CAS
Google Scholar
Zhou XW, Xie M, Hong F, Li QZ (2009) Genomic cloning and characterization of a FIP-gsi gene encoding a fungal immunomodulatory protein from Ganoderma sinense Zhao et al. (Aphyllophoromycetideae). Int J Med Mush 11(1):77–86
Article
CAS
Google Scholar