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Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens

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COX-2 structural analysis and docking studies with gallic acid structural analogues

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Argonaute 8 (AGO8) Mediates the Elicitation of Direct Defenses against Herbivory

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Novel analogs of sulfasalazine as system xc− antiporter inhibitors: Insights from the molecular modeling studies

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Modification of an Anopheles gambiae odorant binding protein to create an array of chemical sensors for detection of drugs

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Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation

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Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and Isoprenoid Metabolism,

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Recombinant production and solution structure of lipid transfer protein from lentil Lens culinaris

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Structural Basis for Cyclization Specificity of Two Azotobacter Type III Polyketide Synthases

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The Crystal Structure of β-Alanine Synthase from Drosophila melanogaster Reveals a Homooctameric Helical Turn-Like Assembly

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Transport of outer membrane lipids in mycobacteria

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In silico Antidiabetic Screening of Borapetoside C, Cordifolioside A and Magnoflorine

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Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

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Computational Tools for Designing Smart Libraries

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A tetrapeptide class of biased analgesics from an Australian fungus targets the µ-opioid receptor

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Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception

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Twelve Positions in a β-Lactamase That Can Expand Its Substrate Spectrum with a Single Amino Acid Substitution

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Retuning Rieske-type Oxygenases to Expand Substrate Range

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Solution Structure of a Repeated Unit of the ABA-1 Nematode Polyprotein Allergen of Ascaris Reveals a Novel Fold and Two Discrete Lipid-Binding Sites

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A Strategic Protein in Cytochrome c Maturation

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Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme

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Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 ofPlasmodium falciparum: a docking and simulation study

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Intrinsic disorder in S100 proteins

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Homology Modeling and Docking Studies of Human Bcl-2L10 Protein

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Classification of a Haemophilus influenzae ABC Transporter HI1470/71 through Its Cognate Molybdate Periplasmic Binding Protein, MolA

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A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani

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Galline Ex-FABP Is an Antibacterial Siderocalin and a Lysophosphatidic Acid Sensor Functioning through Dual Ligand Specificities

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The annotation of full zinc proteomes

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Structural and Functional Characterization of a Ketosteroid Transcriptional Regulator of Mycobacterium tuberculosis

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Multiple Structures for Virtual Ligand Screening: Defining Binding Site Properties-Based Criteria to Optimize the Selection of the Query

Nasr, N. B., Guillemain, H., Lagarde, N., Zagury, J., & Montès, M. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci3004557 · Cited by 39

The deduced role of a chitinase containing two nonsynergistic catalytic domains

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Hydroxyethylamine Based Phthalimides as New Class of Plasmepsin Hits: Design, Synthesis and Antimalarial Evaluation

Singh, A. K., Rathore, S., Tang, Y. B., Goldfarb, N. E., Dunn, B. M., Rajendran, V., Ghosh, P. C., Singh, N., Latha, N., Singh, B. K., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139347 · Cited by 35

Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding

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Structure of the Flavoprotein Tryptophan 2-Monooxygenase, a Key Enzyme in the Formation of Galls in Plants

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Ionizable side chains at catalytic active sites of enzymes

Jimenez‐Morales, D., Liang, J., & Eisenberg, B. (2012) · European Biophysics Journal · doi:10.1007/s00249-012-0798-4 · Cited by 35

Structural Basis for Different Specificities of Acyltransferases Associated with the Human Cytosolic and Mitochondrial Fatty Acid Synthases

Bunkòczi, G., Misquitta, S. A., Wu, X., Lee, W. H., Рожкова, А. М., Kochan, G. T., Kavanagh, K. L., Oppermann, U. C. T., & Smith, S. (2009) · Chemistry & Biology · doi:10.1016/j.chembiol.2009.04.011 · Cited by 35

Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency

Goldfarb, N. E., Ohanessian, M., Biswas, S., McGee, T. D., Mahon, B. P., Ostrov, D. A., Garcia, J., Tang, Y. B., McKENNA, R. V., Roitberg, A. E., et al. (2014) · Biochemistry · doi:10.1021/bi501088e · Cited by 35

Prediction of the responsiveness to pharmacological chaperones: lysosomal human alpha-galactosidase, a case of study

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p21 Exploits Residue Tyr151 as a Tether for High-Affinity PCNA Binding

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Fast dynamics perturbation analysis for prediction of protein functional sites

Ming, D., Cohn, J. D., & Wall, M. E. (2008) · BMC Structural Biology · doi:10.1186/1472-6807-8-5 · Cited by 35

The LabelHash algorithm for substructure matching

Moll, M., Bryant, D., & Kavraki, L. E. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-555 · Cited by 34

Synthesis, biological evaluation, and molecular docking studies of N-(α-acetamido cinnamoyl) aryl hydrazone derivatives as antiinflammatory and analgesic agents

Galla, R., Prasad, K. V. S. R. G., Umamaheswari, A., Pradhan, D., & Bharathi, K. (2014) · Medicinal Chemistry Research · doi:10.1007/s00044-014-1091-0 · Cited by 34

Development of novel (1- H ) benzimidazole bearing pyrimidine-trione based MAO-A inhibitors: Synthesis, docking studies and antidepressant activity

Mathew, B., Suresh, J., & Anbazhagan, S. (2012) · Journal of Saudi Chemical Society · doi:10.1016/j.jscs.2012.09.015 · Cited by 34

Pleiotropic and Epistatic Behavior of a Ring-Hydroxylating Oxygenase System in the Polycyclic Aromatic Hydrocarbon Metabolic Network from Mycobacterium vanbaalenii PYR-1

Weon, H., Kim, S.-J., Kim, D., Kim, J. M., Kim, H.-L., Ahn, Y., Sutherland, J. B., & Cerniglia, C. E. (2014) · Journal of Bacteriology · doi:10.1128/jb.01945-14 · Cited by 34

Structure-Based Identification of Novel Ligands Targeting Multiple Sites within a Chemokine–G-Protein-Coupled-Receptor Interface

Smith, E. W., Nevins, A. M., Qiao, Z., Liu, Y., Getschman, A. E., Vankayala, S. L., Kemp, M. T., Peterson, F. C., Li, R., Volkman, B. F., et al. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b02042 · Cited by 35

Crystal Structure of the Metallo-β-Lactamase GOB in the Periplasmic Dizinc Form Reveals an Unusual Metal Site

Morán-Barrio, J., Lisa, M., Larrieux, N., Drusin, S. I., Viale, A. M., Moreno, D. M., Buschiazzo, A., & Vila, A. J. (2016) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01067-16 · Cited by 34

Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations

Shawon, J., Khan, A. M., Rahman, A., Hoque, M. M., Halim, M. A., Sarwar, M. G., & Halim, M. A. (2016) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-016-0186-3 · Cited by 34

Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins

Luk, H. L., Bhattacharyya, N., Montisci, F., Morrow, J. M., Melaccio, F., Wada, A., Sheves, M., Fanelli, F., Chang, B. S. W., & Olivucci, M. (2016) · Scientific Reports · doi:10.1038/srep38425 · Cited by 35

Epitopes based drug design for dengue virus envelope protein: A computational approach

Wadood, A., Mehmood, A., Khan, H., Ilyas, M., Ahmad, A., Alarjah, M. A., & Abu‐Izneid, T. (2017) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2017.10.008 · Cited by 34

Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds

Kurjogi, M. M., Satapute, P., Jogaiah, S., Abdelrahman, M., Daddam, J. R., Ramu, V., & Tran, L. P. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19010133 · Cited by 34

Untangling the multi-regime molecular mechanism of verbenol-chemotype Zingiber officinale essential oil against Aspergillus flavus and aflatoxin B1

Singh, P. P., Jaiswal, A. K., Kumar, A., Gupta, V. K., & Prakash, B. (2021) · Scientific Reports · doi:10.1038/s41598-021-86253-8 · Cited by 34

Synthesis of Novel Tritopic Hydrazone Ligands: Spectroscopy, Biological Activity, DFT, and Molecular Docking Studies

Rupa, S. A., Moni, M. R., Patwary, M. A. M., Mahmud, M. M., Haque, M. A., Uddin, J., & Abedin, S. M. T. (2022) · Molecules · doi:10.3390/molecules27051656 · Cited by 37

Identification of a natural ligand of the hazel allergen Cor a 1

Jacob, T. P., von Loetzen, C. S., Reuter, A., Lacher, U., Schiller, D., Schobert, R., Mahler, V., Vieths, S., ROSCH, P. J., Schweimer, K., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-44999-2 · Cited by 34

Crystal structure of the variable domain of the Streptococcus gordonii surface protein SspB

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The Crystal Structure of the Extracellular Domain of the Inhibitor Receptor Expressed on Myeloid Cells IREM-1

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A selective, long-lived deep-red emissive ruthenium(II) polypyridine complexes for the detection of BSA

Babu, E., Mareeswaran, P. M., Singaravadivel, S., Bhuvaneswari, J., & Rajagopal, S. (2014) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2014.04.060 · Cited by 34

Computational interaction analysis of organophosphorus pesticides with different metabolic proteins in humans

Sharma, A. K., Gaur, K., Tiwari, R. K., & Gaur, M. S. (2011) · Journal of Biomedical Research · doi:10.1016/s1674-8301(11)60045-6 · Cited by 34

Structural basis for the 4′-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase

Xu, L., Ikeda, H., Liu, L., Arakawa, T., Wakagi, T., Shoun, H., & Fushinobu, S. (2014) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-014-6148-y · Cited by 32

Efficient Identification of Critical Residues Based Only on Protein Structure by Network Analysis

Cusack, M. P., Thibert, B., Bredesen, D. E., & del Rio, G. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000421 · Cited by 34

In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes

Prasad, N. K., Vindal, V., Narayana, S. L., Ramakrishna, V., Kunal, S. P., & Srinivas, M. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1215-0 · Cited by 34

Titanium dioxide nanoparticle–protein interaction explained by docking approach

Ranjan, S., Dasgupta, N., Chinnappan, S., Chidambaram, R., & Kumar, A. (2018) · International Journal of Nanomedicine · doi:10.2147/ijn.s125008 · Cited by 34

Text Mining Improves Prediction of Protein Functional Sites

Verspoor, K. M., Cohn, J. D., Ravikumar, K. E., & Wall, M. E. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032171 · Cited by 33

Discrimination of Ligands with Different Flexibilities Resulting from the Plasticity of the Binding Site in Tubulin

Chakraborti, S., Chakravarty, D., Gupta, S., Chatterji, B. P., Dhar, G., Poddar, A., Panda, D., Chakrabarti, P., Dastidar, S. G., & Bhattacharyya, B. (2012) · Biochemistry · doi:10.1021/bi300474q · Cited by 32

Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa

Domínguez-Gil, T., Lee, M., Acebrón-Ávalos, I., Mahasenan, K. V., Hesek, D., Dik, D. A., Byun, B., Lastochkin, E., Fisher, J. F., Mobashery, S., et al. (2016) · Structure · doi:10.1016/j.str.2016.07.019 · Cited by 33

Protein pocket detection via convex hull surface evolution and associated Reeb graph

Zhao, R., Cang, Z., Tong, Y., & Wei, G. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty598 · Cited by 33

Identification and characterization of a sterically robust phenylalanine ammonia-lyase among 481 natural isoforms through association of in silico and in vitro studies

Rahmatabadi, S. S., Sadeghian, I., Ghasemi, Y., Sakhteman, A., & Hemmati, S. (2018) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2018.12.006 · Cited by 31

Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites

Mishra, S. K., Kandoi, G., & Jernigan, R. L. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25749 · Cited by 33

Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters

Wei, Y., Xiong, Z. J., Li, J., Zou, C., Cairo, C. W., Klassen, J. S., & Privé, G. G. (2019) · Communications Biology · doi:10.1038/s42003-018-0262-9 · Cited by 35

Synthesis of 4-substituted benzyl-2-triazole-linked-tryptamine-paeonol derivatives and evaluation of their selective inhibitions against butyrylcholinesterase and monoamine oxidase-B

Oh, J., Kang, Y., Hwang, J. H., Park, J.-H., Shin, W., Mun, S., Lee, J. U., Yee, S., & Kim, H. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.07.178 · Cited by 33

Carbohydrate binding sites in Candida albicans exo‐β‐1,3‐glucanase and the role of the Phe‐Phe ‘clamp’ at the active site entrance

Patrick, W. M., Nakatani, Y., Cutfield, S. M., Sharpe, M. L., Ramsay, R. J., & Cutfield, J. F. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2010.07869.x · Cited by 33

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

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Structural Studies of IRF4 Reveal a Flexible Autoinhibitory Region and a Compact Linker Domain

Remesh, S. G., Santosh, V., & Escalante, C. R. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.678789 · Cited by 33

Comparative Sequence, Structure and Redox Analyses of Klebsiella pneumoniae DsbA Show That Anti-Virulence Target DsbA Enzymes Fall into Distinct Classes

Kurth, F., Rimmer, K. A., Premkumar, L., Mohanty, B., Duprez, W., Halili, M. A., Shouldice, S. R., Heras, B., Fairlie, D. P., Scanlon, M. J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080210 · Cited by 32

The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-binding Protein FepB

Chu, B. C. H., Otten, R., Krewulak, K. D., Mulder, F. A. A., & Vogel, H. J. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.564021 · Cited by 32

Phylogenetic analysis, homology modelling, molecular dynamics and docking studies of caffeoyl–CoA-O- methyl transferase (CCoAOMT 1 and 2) isoforms isolated from subabul (Leucaena leucocephala)

Pagadala, N. S., Arha, M., Reddy, P. S., Kumar, R. J., Vavilala, S. L., Prashant, S., Reddy, K. J., Khan, B. M., Rawal, S. K., & Kishor, P. B. K. (2008) · Journal of Molecular Modeling · doi:10.1007/s00894-008-0395-8 · Cited by 32

Novel 1, 4-dihydropyridines for L-type calcium channel as antagonists for cadmium toxicity

Saddala, M. S., Kandimalla, R. J. L., Pradeepkiran, J. A., Bhashyam, S. S., & Asupatri, U. R. (2017) · Scientific Reports · doi:10.1038/srep45211 · Cited by 32

Enzymatic analysis, structural study and molecular docking of laccase and catalase from B. subtilis SK1 after textile dye exposure

Kadam, S. K., Tamboli, A. S., Sambhare, S. B., Jeon, B., & Govindwar, S. P. (2018) · Ecological Informatics · doi:10.1016/j.ecoinf.2018.10.003 · Cited by 33

Discovery of Novel New Delhi Metallo-β-Lactamases-1 Inhibitors by Multistep Virtual Screening

Wang, X., Lü, M., Shi, Y., Ou, Y., & Cheng, X. (2015) · PLoS ONE · doi:10.1371/journal.pone.0118290 · Cited by 32

Computational Analysis of Protein Hotspots

Yang, C., & Wang, S. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100026a · Cited by 32

Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions

Dehury, B., Patra, M. C., Maharana, J., Sahu, J., Sen, P., Modi, M. K., Choudhury, M. D., & Barooah, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097852 · Cited by 32

Dissecting the Role of Critical Residues and Substrate Preference of a Fatty Acyl-CoA Synthetase (FadD13) of Mycobacterium tuberculosis

Khare, G., Gupta, V., Gupta, R. K., Gupta, R., Bhat, R., & Tyagi, A. K. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008387 · Cited by 32

Homologous gene clusters of nicotine catabolism, including a new ω-amidase for α-ketoglutaramate, in species of three genera of Gram-positive bacteria

Cobzaru, C., Ganas, P., Mihăşan, M., Schleberger, P., & Brandsch, R. (2011) · Research in Microbiology · doi:10.1016/j.resmic.2011.01.001 · Cited by 32

Comparative docking and ADMET study of some curcumin derivatives and herbal congeners targeting β-amyloid

Singh, D. B., Gupta, M., Kesharwani, R. K., & Misra, K. (2013) · Network Modeling Analysis in Health Informatics and Bioinformatics · doi:10.1007/s13721-012-0021-7 · Cited by 32

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns

Tseng, Y. Y., Dupree, C., Chen, Z. J., & Li, W. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp308 · Cited by 32

Unusual Water-mediated Antigenic Recognition of the Proinflammatory Cytokine Interleukin-18

Argiriadi, M. A., Xiang, T., Wu, C., Ghayur, T., & Borhani, D. W. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.023887 · Cited by 32

Protein–Protein Docking in Drug Design and Discovery

Kaczor, A. A., Bartuzi, D., Stępniewski, T. M., Matosiuk, D., & Selent, J. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7756-7_15 · Cited by 33

Molecular docking and simulation studies of 3‐(1‐chloropiperidin‐4‐yl)‐6‐fluoro benzisoxazole 2 against VP26 and VP28 proteins of white spot syndrome virus

Sundarrajan, S., Reddy, C. B. R., Dinesh, S., Reddy, S. R., Arumugam, M., Itami, T., & Sudhakaran, R. (2016) · Journal of Fish Diseases · doi:10.1111/jfd.12454 · Cited by 31

Nanoparticle Fullerene (C60) demonstrated stable binding with antibacterial potential towards probable targets of drug resistantSalmonella typhi– a computational perspective andin vitroinvestigation

Skariyachan, S., Parveen, A., & Garka, S. (2016) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2016.1257441 · Cited by 32

Evolution, structure and membrane association of NDUFAF6, an assembly factor for NADH:ubiquinone oxidoreductase (Complex I)

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Stereotyped antibody responses target posttranslationally modified gluten in celiac disease

Snir, O., Chen, X., Gidoni, M., du Pré, M. F., Zhao, Y., Steinsbø, Ø., Lundin, K. E. A., Yaari, G., & Sollid, L. M. (2017) · JCI Insight · doi:10.1172/jci.insight.93961 · Cited by 31

Role of pncA gene mutations W68R and W68G in pyrazinamide resistance

Aggarwal, M., Singh, A. P., Grover, S., Pandey, B., Kumari, A., & Grover, A. (2017) · Journal of Cellular Biochemistry · doi:10.1002/jcb.26420 · Cited by 31

Designing of phenol-based β−carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach

Ahamad, S., Hassan, M. I., & Dwivedi, N. (2018) · 3 Biotech · doi:10.1007/s13205-018-1278-z · Cited by 31

Biocontrol and non-target effect of fractions and compound isolated from Streptomyces rimosus on the immature stages of filarial vector Culex quinquefasciatus Say (Diptera: Culicidae) and the compound interaction with Acetylcholinesterase (AChE1)

Ganesan, P., Stalin, A., Paulraj, M. G., Balakrishna, K., Savarimuthu Ignacimuthu, S. J., & Al-Dhabi, N. A. (2018) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2018.05.061 · Cited by 33

Curative effect of arjunolic acid from Terminalia arjuna in non-alcoholic fatty liver disease models

Toppo, E., Darvin, S. S., Esakkimuthu, S., Buvanesvaragurunathan, K., Krishna, T. P. A., Caesar, S. A., Stalin, A., Balakrishna, K., Pandikumar, P., Savarimuthu Ignacimuthu, S. J., et al. (2018) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2018.08.019 · Cited by 31

A novel protein descriptor for the prediction of drug binding sites

Jiang, M., Li, Z., Bian, Y., & Wei, Z. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3058-0 · Cited by 31

CASTp: Computed Atlas of Surface Topography of proteins

Binkowski, T. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg512 · Cited by 1,693

CASTp 3.0: computed atlas of surface topography of proteins

Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky473 · Cited by 2,389

CASTp 3.0: Computed Atlas of Surface Topography of Proteins and Beyond

Tian, W., Chen, C., & Liang, J. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2017.11.325 · Cited by 39

CASTpFold: Computed Atlas of Surface Topography of alpha-folded proteins

Ye, B., Tian, W., Wang, B., & Liang, J. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2023.11.2061 · Cited by 1

CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds

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