RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020) · Science · doi:10.1126/science.abb2507 · Cited by 8,897

Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein

Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586

DrugBank 5.0: a major update to the DrugBank database for 2018

Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1037 · Cited by 8,404

UniProt: a worldwide hub of protein knowledge

The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357

The Pfam protein families database: towards a more sustainable future

Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1344 · Cited by 5,975

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The GTEx Consortium, Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., et al. (2020) · Science · doi:10.1126/science.aaz1776 · Cited by 5,547

BiRDS - Binding Residue Detection from Protein Sequences Using Deep ResNets

Chelur, V., & Priyakumar, U. D. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00972 · Cited by 19

Exploring protein symmetry at the RCSB Protein Data Bank

Duarte, J. M., Dutta, S., Goodsell, D. S., & Burley, S. K. (2022) · Emerging Topics in Life Sciences · doi:10.1042/etls20210267 · Cited by 26

Profiling prediction of nuclear receptor modulators with multi-task deep learning methods: toward the virtual screening

Wang, J., Lou, C., Liu, G., Li, W., Wu, Z., & Tang, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac351 · Cited by 20

Novel mechanism of napabucasin, a naturally derived furanonaphthoquinone: apoptosis and autophagy induction in lung cancer cells through direct targeting on Akt/mTOR proteins

Petsri, K., Thongsom, S., Racha, S., Chamni, S., Jindapol, S., Kaekratoke, N., Zou, H., & Pithi Chanvorachote, B. (2022) · BMC Complementary Medicine and Therapies · doi:10.1186/s12906-022-03727-6 · Cited by 20

Bioinformatics tools and data resources for assay development of fluid protein biomarkers

Waury, K., Willemse, E. A. J., Vanmechelen, E., Zetterberg, H., Teunissen, C. E., & Abeln, S. (2022) · Biomarker Research · doi:10.1186/s40364-022-00425-w · Cited by 20

Cryo-EM structure of ex vivo fibrils associated with extreme AA amyloidosis prevalence in a cat shelter

Schulte, T. P., Chaves-Sanjuán, A., Mazzini, G., Speranzini, V., Lavatelli, F., Ferri, F., Palizzotto, C., Mazza, M., Milani, P., Nuvolone, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34743-2 · Cited by 20

Network Pharmacology and Experimental Validation to Explore the Effect and Mechanism of Kanglaite Injection Against Triple-Negative Breast Cancer

Zhao, M., Fu, L., Xu, P., Wang, T., & Li, P. (2023) · Drug Design Development and Therapy · doi:10.2147/dddt.s397969 · Cited by 20

The Plasmodium falciparum apicoplast cysteine desulfurase provides sulfur for both iron-sulfur cluster assembly and tRNA modification

Swift, R., Elahi, R., Rajaram, K., Liu, H. B., & Prigge, S. T. (2023) · eLife · doi:10.7554/elife.84491 · Cited by 26

Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Strauss, J., Deng, L., Gao, S., Toseland, A., Bachy, C., Zhang, C., Kirkham, A. R., Hopes, A., Utting, R., Joest, E. F., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01498-5 · Cited by 20

LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria

Augustijn, H. E., Karapliafis, D., Joosten, K., Rigali, S., van Wezel, G. P., & Medema, M. H. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168558 · Cited by 20

Collision Cross Sections for Native Proteomics: Challenges and Opportunities

Ruotolo, B. T. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00686 · Cited by 20

Artificial intelligence analysis to explore synchronize exercise, cobalamin, and magnesium as new actors to therapeutic of migraine symptoms: a randomized, placebo-controlled trial

Matin, H., Taghian, F., & Chitsaz, A. (2022) · Neurological Sciences · doi:10.1007/s10072-021-05843-6 · Cited by 20

Artificial Intelligence Transforming Post-Translational Modification Research

Kim, D. N., Yin, T., Zhang, T., Im, A. K., Cort, J., Rozum, J. C., Pollock, D. D., Qian, W., & Feng, S. (2024) · Bioengineering · doi:10.3390/bioengineering12010026 · Cited by 19

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Gaber, A., & Pavšič, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22169081 · Cited by 22

β-lactoglobulin conformation influences its interaction with caffeine

Rosa, L. N. S., Rezende, J. D. P., Coelho, Y. L., Mendes, T. A. D. O., da Silva, L. H. M., & Pires, A. C. D. S. (2021) · Food Bioscience · doi:10.1016/j.fbio.2021.101418 · Cited by 19

Network Pharmacology and Molecular Docking Analysis on Pharmacological Mechanisms of Astragalus membranaceus in the Treatment of Gastric Ulcer

Zhou, P., Zhou, R., Yao, M., An, L., Wang, F., & Du, Q. (2022) · Evidence-based Complementary and Alternative Medicine · doi:10.1155/2022/9007396 · Cited by 19

Introduction to Plant Metabolism, Secondary Metabolites Biosynthetic Pathway, and In-Silico Molecular Docking for Determination of Plant Medicinal Compounds: An Overview

Dhaniaputri, R., Suwono, H., Amin, M., & Lukiati, B. (2022) · Advances in biological sciences research/Advances in Biological Sciences Research · doi:10.2991/absr.k.220406.053 · Cited by 19

The type III polyketide synthase supergene family in plants: complex evolutionary history and functional divergence

Guo, D., Wang, H., Zhang, S., & Lan, T. (2022) · The Plant Journal · doi:10.1111/tpj.15953 · Cited by 19

Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study

Adedeji, E. O., Oduselu, G. O., Ogunlana, O. O., Fatumo, S., Koenig, R., & Adebiyi, E. F. (2022) · Insects · doi:10.3390/insects13111070 · Cited by 19

A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea

Xu, X., Shen, Y., Zhang, Y., Li, Q., Wang, W., Chen, L., Chen, G., Ng, W. L., Islam, M. N., Punnarak, P., et al. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2022.1075353 · Cited by 19

Design, synthesis, and biological activity of dual monoamine oxidase A and heat shock protein 90 inhibitors, N-Methylpropargylamine-conjugated 4-isopropylresorcinol for glioblastoma

Tseng, H.-J., Banerjee, S., Qian, B., Lai, M.-J., Wu, T.-Y., Hsu, T., Lin, T. E., Hsu, K., Chuang, K., Liou, J., et al. (2023) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2023.115459 · Cited by 19

IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models

Pang, Y., & Liu, B. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011657 · Cited by 19

Geniposide effectively safeguards HT22 cells against Aβ-induced damage by activating mitophagy via the PINK1/Parkin signaling pathway

Ye, J., Wu, J., Ai, L., Zhu, M., Li, Y., Yin, D., & Huang, Q. (2024) · Biochemical Pharmacology · doi:10.1016/j.bcp.2024.116296 · Cited by 20

Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure

Zhao, N., Wu, T., Wang, W., Zhang, L., & Gong, X. (2024) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-024-00626-x · Cited by 20

GC–MS analysis, molecular docking, and pharmacokinetic studies on Dalbergia sissoo barks extracts for compounds with anti-diabetic potential

Vijh, D., & Gupta, P. (2024) · Scientific Reports · doi:10.1038/s41598-024-75570-3 · Cited by 19

Global profiling of protein complex dynamics with an experimental library of protein interaction markers

Dörig, C., Marulli, C., Peskett, T. R., Volkmar, N., Pantolini, L., Studer, G., Paleari, C., Frommelt, F., Schwede, T. F., de Souza, N., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02432-8 · Cited by 20

Combined machine learning models, docking analysis, ADMET studies and molecular dynamics simulations for the design of novel FAK inhibitors against glioblastoma

Zhao, Y., He, X., & Wan, Q. (2024) · BMC Chemistry · doi:10.1186/s13065-024-01316-x · Cited by 18

Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV ‐2 neutralizing antibody complexes

Sharma, D., Rawat, P., Vani, J., & Gromiha, M. M. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26277 · Cited by 17

An immunoinformatics-based designed multi-epitope candidate vaccine (mpme-VAC/STV-1) against Mycoplasma pneumoniae

Rodrigues, T. C. V., Jaiswal, A. K., Lemes, M. R., da Silva, M. V., Sales‐Campos, H., Alcântara, L. C. J., Tosta, S. F. D. O., Kato, R. B., Alzahrani, K. J., Barh, D., et al. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.105194 · Cited by 18

Integrated Metabolomics and Network Pharmacology Revealed Hong-Hua-Xiao-Yao Tablet’s Effect of Mediating Hormone Synthesis in the Treatment of Mammary Gland Hyperplasia

Gao, Z., Mi, R., Cheng, Z., Li, X., Zeng, H., Wu, G., Zhao, J., Zhang, W., & Ye, J. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.788019 · Cited by 18

Exploring the Anti-inflammatory Effects of Protopine Total Alkaloids of Macleaya Cordata (Willd.) R. Br.

Dong, Z., Wang, Y., Tang, Z., Li, C., Jiang, T., Yang, Z., & Zeng, J. (2022) · Frontiers in Veterinary Science · doi:10.3389/fvets.2022.935201 · Cited by 18

HProteome-BSite: predicted binding sites and ligands in human 3D proteome

Sim, J., Kwon, S., & Seok, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac873 · Cited by 18

6-Shogaol Exhibits Anti-viral and Anti-inflammatory Activity in COVID-19-Associated Inflammation by Regulating NLRP3 Inflammasomes

Kode, J., Maharana, J., Dar, A. A., Mukherjee, S., Gadewal, N. S., Sigalapalli, D. K., Kumar, S., Panda, D., Ghosh, S., Keshry, S. S., et al. (2023) · ACS Omega · doi:10.1021/acsomega.2c07138 · Cited by 18

Bioinformatics and In silico approaches to identify novel biomarkers and key pathways for cancers that are linked to the progression of female infertility: A comprehensive approach for drug discovery

Hossain, M. A., Sohel, M., Rahman, M. H., Hasan, M. I., Khan, M. S., Amin, M. A., Islam, M. Z., & Peng, S. (2023) · PLoS ONE · doi:10.1371/journal.pone.0265746 · Cited by 18

Breaking free from the crystal lattice: Structural biology in solution to study protein degraders

Haubrich, K., Spiteri, V. A., Farnaby, W., Sobott, F., & Ciulli, A. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102534 · Cited by 19

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

Wang, J. Y., Khmelinskaia, A., Sheffler, W., Miranda, M. C., Antanasijevic, A., Borst, A. J., Torres, S. V., Shu, C., Hsia, Y., Nattermann, U., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2214556120 · Cited by 17

Two MP2CL5 Antigen Vaccines from Naegleria fowleri Stimulate the Immune Response against Meningitis in the BALB/c Model

Gutiérrez‐Sánchez, M., Carrasco‐Yépez, M. M., Correa‐Basurto, J., Ramírez-Salinas, G. L., & Hernández, S. R. (2023) · Infection and Immunity · doi:10.1128/iai.00181-23 · Cited by 18

Multivalent Carbohydrate Nanocomposites for Tumor Microenvironment Remodeling to Enhance Antitumor Immunity

Hyun, G. H., Jeong, D., Yang, Y. Y., Cho, I. H., Ha, Y., Xing, X., Abbott, D. W., Hsieh, Y. S. Y., Kang, Y. P., Cha, J., et al. (2023) · ACS Nano · doi:10.1021/acsnano.3c01645 · Cited by 18

Qijiao Shengbai Capsule alleviated leukopenia by interfering leukotriene pathway: Integrated network study of multi-omics

Ma, C., Zhao, J., Zheng, G., Wu, S., Wu, R., Yu, D., Liao, J., Zhang, H., Liu, L., Jiang, L., et al. (2024) · Phytomedicine · doi:10.1016/j.phymed.2024.155424 · Cited by 19

MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

Chen, K., Litfin, T., Singh, J., Zhan, J., & Zhou, Y. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae018 · Cited by 25

Narciclasine suppresses esophageal cancer cell proliferation and migration by inhibiting the FAK signaling pathway

Qiu, Y., Fang, B., Thủy, N. T. T., Li, A., Yoo, H. M., Zheng, X., & Cho, N. (2022) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2021.174669 · Cited by 18

In Vitro and In Silico Evaluation of ACE2 and LOX Inhibitory Activity of Origanum Essential Oils and Carvacrol

Demi̇rci̇, F., Teralı, K., Karadağ, A. E., Biltekin, S. N., Ak-sakallı, E., Demırcı, B., Koşar, M., & Başer, K. H. C. (2022) · Planta Medica · doi:10.1055/a-1828-2479 · Cited by 18

Discovery of Anticancer Activity of Amentoflavone on Esophageal Squamous Cell Carcinoma: Bioinformatics, Structure-Based Virtual Screening, and Biological Evaluation

Chen, L., Fang, B., Qiao, L., & Zheng, Y. (2022) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2203.03050 · Cited by 18

Mechanisms of Cardiorenal Protection With SGLT2 Inhibitors in Patients With T2DM Based on Network Pharmacology

Wang, A., Li, Z., Zhuo, S., Gao, F., Zhang, H., Zhang, Z., Ren, G., & Ma, X. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.857952 · Cited by 19

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

(2023) · doi:10.1093/nar/gkad1012 · Cited by 17

Two newly established and mutually related subfamilies GH13_48 and GH13_49 of the α-amylase family GH13

Mareček, F., Terrapon, N., & Janeĉek, Ŝ. (2024) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-024-13251-x · Cited by 17

Advancements in contemporary pharmacological innovation: Mechanistic insights and emerging trends in drug discovery and development

Majumder, S., & Panigrahi, G. K. (2024) · Intelligent Pharmacy · doi:10.1016/j.ipha.2024.10.001 · Cited by 21

Structural biology in the time of COVID-19: perspectives on methods and milestones

Lynch, M. L., Snell, E. H., & Bowman, S. E. J. (2021) · IUCrJ · doi:10.1107/s2052252521003948 · Cited by 18

Molecular Basis of Ca(II)-Induced Tetramerization and Transition-Metal Sequestration in Human Calprotectin

Silvers, R., Stephan, J. R., Griffin, R. G., & Nolan, E. M. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c06402 · Cited by 17

Mining anion–aromatic interactions in the Protein Data Bank

Kuźniak, E., Glanowski, M., Kurczab, R., Bojarski, A. J., & Podgajny, R. (2022) · Chemical Science · doi:10.1039/d2sc00763k · Cited by 17

Screening and Identification of HBV Epitopes Restricted by Multiple Prevalent HLA-A Allotypes

Ding, Y., Zhou, Z., Li, X., Zhao, C., Jin, X., Liu, X. K., Wu, Y., Mei, X., Li, J., Qiu, J., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.847105 · Cited by 17

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

Robin, V., Bodein, A., Scott‐Boyer, M., Leclercq, M., Périn, O., & Droit, A. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.962799 · Cited by 19

Base-specific RNA force field improving the dynamics conformation of nucleotide

Li, Z., Mu, J., Chen, J., & Chen, H. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.09.183 · Cited by 18

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

Guvench, O. (2022) · Molecules · doi:10.3390/molecules27217276 · Cited by 18

Cyclic peptides as an inhibitor of metastasis in breast cancer targeting MMP-1: Computational approach

Hasan, M. M., Shawon, A. R. M., Aeyas, A., & Uddin, M. A. (2022) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2022.101128 · Cited by 16

CIPDB: A biological structure databank for studying cation and π interactions

Yang, J., Wang, F., Wang, M., Wang, D., Zhou, Z., Hao, G., Li, Q. X., & Yang, G. (2023) · Drug Discovery Today · doi:10.1016/j.drudis.2023.103546 · Cited by 18

Coenzyme A binding sites induce proximal acylation across protein families

Carrico, C., Cruz, A., Walter, M., Meyer, J. G., Wehrfritz, C., Shah, S., Wei, L., Schilling, B., & Verdin, E. M. (2023) · Scientific Reports · doi:10.1038/s41598-023-31900-5 · Cited by 18

Therapeutic effects and mechanism of action of lavender essential oil on atopic dermatitis by modulating the STAT3/RORγt pathway

Duan, J., Li, J., Wang, Y., Zhou, P., Wang, X., Xia, N., Wang, J., Li, J., Wang, W., Wang, X., et al. (2023) · Arabian Journal of Chemistry · doi:10.1016/j.arabjc.2023.105525 · Cited by 17

Lactylation prediction models based on protein sequence and structural feature fusion

Yang, Y., Yang, J., & Liu, J.-F. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbad539 · Cited by 17

KEGG orthology prediction of bacterial proteins using natural language processing

Chen, J., Wu, H., & Wang, N. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05766-x · Cited by 17

RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens

Goodsell, D. S., & Burley, S. K. (2021) · Structure · doi:10.1016/j.str.2021.10.008 · Cited by 17

Integrated metabolomics and network pharmacology to reveal the therapeutic mechanism of Dingkun Pill on polycystic ovary syndrome

Cai, Y., Zhang, F., Dou, X., Zeng, H., Wu, G., Liang, Y., Xu, X., Zhao, J., Ye, J., & Zhang, W. (2022) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2022.115442 · Cited by 17

A multiomics and network pharmacological study reveals the neuroprotective efficacy of Fu-Fang-Dan-Zhi tablets against glutamate-induced oxidative cell death

Gu, Y., Huang, P., Cheng, T.-F., Yang, J., Wu, G., Sun, Y., Liu, A., Li, H., Zhao, J., & Ye, J. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105873 · Cited by 16

Explaining Conformational Diversity in Protein Families through Molecular Motions

Lombard, V., Grudinin, S., & Laine, É. (2024) · Scientific Data · doi:10.1038/s41597-024-03524-5 · Cited by 20

UniLectin, A One‐Stop‐Shop to Explore and Study Carbohydrate‐Binding Proteins

Imberty, A., Bonnardel, F., & Lisacek, F. (2021) · Current Protocols · doi:10.1002/cpz1.305 · Cited by 15

A Closer Look at Dexamethasone and the SARS-CoV-2-Induced Cytokine Storm: In Silico Insights of the First Life-Saving COVID-19 Drug

Morgan, P. M., Arnold, S. J., Hsiao, N., & Shu, C. (2021) · Antibiotics · doi:10.3390/antibiotics10121507 · Cited by 16

Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics

Hellemann, E., Walker, J. L., Lesko, M. A., Chandrashekarappa, D. G., Schmidt, M. C., O’Donnell, A. F., & Durrant, J. D. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009929 · Cited by 16

Design, synthesis and anti-tumor activity of novel benzothiophenonaphthalimide derivatives targeting mitochondrial DNA (mtDNA) G-quadruplex.

Huang, Q., Wang, X., Cheng, A., Zhang, H., Yu, Q.-M., Shen, C.-F., Awadasseid, A., Zhao, X., Xiong, X., Wu, Y.-L., et al. (2022) · Biochemical Pharmacology · doi:10.1016/j.bcp.2022.115062 · Cited by 14

Prediction of Protein Allosteric Signalling Pathways and Functional Residues Through Paths of Optimised Propensity

Wu, N., Yaliraki, S. N., & Barahona, M. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167749 · Cited by 16

Investigation of the Fluorescence Turn-off Mechanism, Genome, Molecular Docking In Silico and In Vitro Studies of 2‑Acetyl‑3 H ‑benzo[ f ]chromen-3-one

Koppal, V. V., Melavanki, R. M., Kusanur, R. A., Bagewadi, Z. K., Yaraguppi, D. A., Deshpande, S., & Patil, N. R. (2022) · ACS Omega · doi:10.1021/acsomega.2c02424 · Cited by 16

Sesquiterpene lactones from Artemisia vulgaris L. as potential NO inhibitors in LPS-induced RAW264.7 macrophage cells

Chen, X., Liu, T., Hu, Y., Qiao, T.-T., Wu, X., Sun, P., Qian, C.-W., Ren, Z., Zheng, J., & Wang, Y. (2022) · Frontiers in Chemistry · doi:10.3389/fchem.2022.948714 · Cited by 16

Artificial intelligence methods enhance the discovery of RNA interactions

Pepe, G., Appierdo, R., Carrino, C., Ballesio, F., Helmer‐Citterich, M., & Gherardini, P. F. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1000205 · Cited by 16

20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening

Lynch, M. L., Snell, M. E., Potter, S. A., Snell, E. H., & Bowman, S. E. J. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798323001274 · Cited by 16

Mechanism of skin whitening through San-Bai decoction-induced tyrosinase inhibition and discovery of natural products targeting tyrosinase

Li, L., Tang, Y., Li, X., Zhou, T., Song, Q., & Li, A. (2023) · Medicine · doi:10.1097/md.0000000000033420 · Cited by 16

Discovery of the first-in-class potent and isoform-selective human carbonic anhydrase III inhibitors

Giovannuzzi, S., Bonardi, A., Gratteri, P., Nocentini, A., & Supuran, C. T. (2023) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2023.2202360 · Cited by 16

AI-Predicted mTOR Inhibitor Reduces Cancer Cell Proliferation and Extends the Lifespan of C. elegans

Vidović, T., Dakhovnik, A., Hrabovskyi, O., MacArthur, M. R., & Ewald, C. Y. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24097850 · Cited by 16

Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon

Skalidis, I., Kyrilis, F. L., Tüting, C., Hamdi, F., Träger, T. K., Belapure, J., Hause, G., Fratini, M., O’Reilly, F. J., Heilmann, I., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-04885-0 · Cited by 16

Network pharmacology prediction and molecular docking-based strategy to discover the potential pharmacological mechanism of Huang–Qi–Gui–Zhi–Wu–Wu decoction against deep vein thrombosis

Fan, W., Lan, S., Yang, Y., & Liang, J. (2023) · Journal of Orthopaedic Surgery and Research · doi:10.1186/s13018-023-03948-6 · Cited by 16

A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice

Shim, K.-C., Kang, Y., Song, J., Kim, Y. J., Kim, J. K., Kim, C., Tai, T. H., Park, I., & Ahn, S.-N. (2023) · Plants · doi:10.3390/plants12152831 · Cited by 16

TransGEM: a molecule generation model based on Transformer with gene expression data

Liu, Y., Yu, H., Duan, X., Zhang, X., Cheng, T., Jiang, F., Tang, H., Ruan, Y., Zhang, M., Zhang, H., et al. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae189 · Cited by 16

Benzoxaborinine, New Chemotype for Carbonic Anhydrase Inhibition: Ex Novo Synthesis, Crystallography, In Silico Studies, and Anti-Melanoma Cell Line Activity.

Giovannuzzi, S., Ņikitjuka, A., Angeli, A., Smietana, M., Massardi, M., Turati, M., Ronca, R., Bonardi, A., Nocentini, A., Ferraroni, M., et al. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c01516 · Cited by 11

Esterase-2 mutant-based nanostructured amperometric biosensors for the selective determination of paraoxon (Neurotoxin)

Magar, H. S., Fayez, M., Febbraio, F., & Hassan, R. Y. A. (2024) · Analytical Biochemistry · doi:10.1016/j.ab.2024.115751 · Cited by 16

Labdane Diterpenoids from Salvia tingitana Etl. Synergize with Clindamycin against Methicillin-Resistant Staphylococcus aureus

Iobbi, V., Brun, P., Bernabé, G., Kentsop, R. A. D., Donadio, G., Ruffoni, B., Fossa, P., Bisio, A., & Tommasi, N. D. (2021) · Molecules · doi:10.3390/molecules26216681 · Cited by 16

Investigating the Effects of Amino Acid Variations in Human Menin

Biancaniello, C., D’Argenio, A., Giordano, D., Dotolo, S., Scafuri, B., Marabotti, A., d’Acierno, A., Tagliaferri, R., & Facchiano, A. M. (2022) · Molecules · doi:10.3390/molecules27051747 · Cited by 17

DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design

Liu, Y., Gan, J., Wang, R., Yang, X., Xiao, Z. J., & Cao, Y. (2022) · Molecules · doi:10.3390/molecules27030683 · Cited by 17

De novo drug design framework based on mathematical programming method and deep learning model

Zhao, Y., Liu, Q., Wu, X., Zhang, L., Du, J., & Meng, Q. (2022) · AIChE Journal · doi:10.1002/aic.17748 · Cited by 17

Mixed computational-experimental study to reveal the anti-metastasis and anti-angiogenesis effects of Astragalin in human breast cancer

Tian, S., Wei, Y., Hu, H., & Zhao, H. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.106131 · Cited by 16

Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli

Gong, W., Guerler, A., Zhang, C., Warner, E., Li, C., & Zhang, Y. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166944 · Cited by 13

Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences

Basu, S., Jing, Y., Kihara, D., & Kurgan, L. (2024) · Briefings Bioinform. · doi:10.1093/bib/bbaf016 · Cited by 15

BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation

Baldazzi, D., Savojardo, C., Martelli, P. L., & Casadio, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab328 · Cited by 15

Computer‐Guided Trypanocidal Activity of Natural Lactones Produced by Endophytic Fungus of Euphorbia umbellata

Gusmão, A. S., Abreu, L. S., Tavares, J. F., de Freitas, H. F., Pita, S. S. D. R., Gonçalves-Santos, E., Caldas, I. S., Vieira, A. A., & Silva, E. D. O. (2021) · Chemistry & Biodiversity · doi:10.1002/cbdv.202100493 · Cited by 16

Bioinformatics study of the potential therapeutic effects of ginsenoside Rf in reversing nonalcoholic fatty liver disease

Chen, L.-C., Wang, L., Ao, W., Chen, Y., Li, S., Huang, Z., Yu, D., Dong, Y., Gu, J., & Zeng, H. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.112879 · Cited by 15

Actions of Novel Angiotensin Receptor Blocking Drugs, Bisartans, Relevant for COVID-19 Therapy: Biased Agonism at Angiotensin Receptors and the Beneficial Effects of Neprilysin in the Renin Angiotensin System

Moore, G. J., Ridgway, H. F., Kelaidonis, K., Chasapis, C. T., Ligielli, I., Mavromoustakos, T., Bojarska, J., & Matsoukas, J. (2022) · Molecules · doi:10.3390/molecules27154854 · Cited by 15

MPAD: A Database for Binding Affinity of Membrane Protein–protein Complexes and their Mutants

Ridha, F., Kulandaisamy, A., & Gromiha, M. M. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167870 · Cited by 15

Bioassay-guided isolation and characterization of lead antimicrobial compounds from Acacia hydaspica plant extract

Afsar, T., Razak, S., Almajwal, A. M., Shabbir, M., Khan, K., Trembley, J. H., & Alruwaili, N. W. (2022) · AMB Express · doi:10.1186/s13568-022-01501-y · Cited by 16

Pharmacological Mechanism of Aucklandiae Radix against Gastric Ulcer Based on Network Pharmacology and In Vivo Experiment

Feng, L., Lisha, A., Li, H., Mu, X., Ta, N., Bai, L., Fu, M., & Chen, Y. (2023) · Medicina · doi:10.3390/medicina59040666 · Cited by 15

Intrinsic disorder and flexibility in proteins: a challenge for structural biology and drug design

Zanotti, G. (2023) · Crystallography Reviews · doi:10.1080/0889311x.2023.2208518 · Cited by 16

AI-Aided Search for New HIV-1 Protease Ligands

Arrigoni, R., Santacroce, L., Ballini, A., & Palese, L. L. (2023) · Biomolecules · doi:10.3390/biom13050858 · Cited by 15

Residue-level error detection in cryoelectron microscopy models

Reggiano, G., Lugmayr, W., Farrell, D. P., Marlovits, T. C., & DiMaio, F. (2023) · Structure · doi:10.1016/j.str.2023.05.002 · Cited by 14

Mechanisms of ssDNA aptamer binding to Cd2+ in aqueous solution: A molecular dynamics study

Wu, X., Yuan, H., Zhao, R., Wang, P., Yuan, M., Cao, H., Ye, T., & Xu, F. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.126412 · Cited by 15

RCSB Protein Data Bank: celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Burley, S. K. (2021) · Acta Crystallographica Section A Foundations and Advances · doi:10.1107/s0108767321090310 · Cited by 18

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C. H., Dalenberg, K., Duarte, J. M., Dutta, S., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1004 · Cited by 1,268

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

Burley, S. K., Piehl, D. W., Vallat, B. K., & Zardecki, C. (2024) · IUCrJ · doi:10.1107/s2052252524002604 · Cited by 64

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P., Crichlow, G. V., Dalenberg, K., Duarte, J. M., et al. (2022) · Protein Science · doi:10.1002/pro.4482 · Cited by 123

The RCSB Protein Data Bank: new resources for research and education

Rose, P. W., Bi, C., Bluhm, W. F., Christie, C. H., Dimitropoulos, D., Dutta, S., Green, R. K., Goodsell, D. S., Prlić, A., Quesada, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1200 · Cited by 535