RPBS: a web resource for structural bioinformatics

The Protein Data Bank

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The Ensembl genome database project

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Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives

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A Model for High-Order Markov Chains

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Crystallographic refinement by simulated annealing

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Modeling structurally variable regions in homologous proteins with rosetta

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PDB-based protein loop prediction: parameters for selection and methods for optimization

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CODA: A combined algorithm for predicting the structurally variable regions of protein models

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Assessing the performance of fold recognition methods by means of a comprehensive benchmark.

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Evaluation of protein fold comparison servers

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High accuracy prediction of β‐turns and their types using propensities and multiple alignments

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New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification 1 1Edited by J. M. Thornton

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A Global Taxonomy of Loops in Globular Proteins

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YAKUSA: A fast structural database scanning method

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Predicting the disulfide bonding state of cysteines using protein descriptors

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Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides

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PredAcc: prediction of solvent accessibility.

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SA-Search: a web tool for protein structure mining based on a Structural Alphabet

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SCit: web tools for protein side chain conformation analysis

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Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS

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Automat and BLAST: comparison of two protein sequence similarity search programs

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Filtering Redundancies For Sequence Similarity Search Programs

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Experimental demonstration of highly reliable dynamic memristor for artificial neuron and neuromorphic computing

Park, S.-O., Jeong, H., Park, J., Bae, J., & Choi, S. (2022) · Nature Communications · doi:10.1038/s41467-022-30539-6 · Cited by 331

Mobyle: a new full web bioinformatics framework

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MTiOpenScreen: a web server for structure-based virtual screening

Labbé, C. M., Rey, J., Lagorce, D., Vavruša, M., Becot, J., Spérandio, O., Villoutreix, B. O., Tufféry, P., & Miteva, M. A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv306 · Cited by 301

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

Sauton, N., Lagorce, D., Villoutreix, B. O., & Miteva, M. A. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-184 · Cited by 139

Proceedings of the 35th European Peptide Symposium

Bonnet, D. (2018) · doi:10.17952/35eps · Cited by 124

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Ropp, P. J., Spiegel, J. O., Walker, J. L., Green, H., Morales, G. A., Milliken, K. A., Ringe, J. J., & Durrant, J. D. (2019) · Journal of Cheminformatics · doi:10.1186/s13321-019-0358-3 · Cited by 100

Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach

Mondal, S. I., Ferdous, S., Akter, A., Mahmud, Z., Karim, N., Islam, M. M., Jewel, N. A., & Afrin, T. (2015) · Advances and Applications in Bioinformatics and Chemistry · doi:10.2147/aabc.s88522 · Cited by 94

Molecularly Imprinted Polymer Nanoparticles as Potential Synthetic Antibodies for Immunoprotection against HIV

Xu, J., Merlier, F., Avalle, B., Vieillard, V., Debré, P., Haupt, K., & Bui, B. T. S. (2019) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.8b22732 · Cited by 93

Local Protein Structures

Offmann, B., Tyagi, M., & de Brevern, A. (2007) · Current Bioinformatics · doi:10.2174/157489307781662105 · Cited by 96

Advances in epitope molecularly imprinted polymers for protein detection: a review

Wang, X., Chen, G., Zhang, P., & Jia, Q. (2021) · Analytical Methods · doi:10.1039/d1ay00067e · Cited by 77

Development of a novel short 12-meric papiliocin-derived peptide that is effective against Gram-negative sepsis

Kim, J., Jacob, B., Jang, M., Kwak, C., Lee, Y., Son, K., Lee, S., Jung, I. D., Jeong, M. S., Kwon, S., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-40577-8 · Cited by 54

Functionalization of Mesoporous Silica Nanoparticles with a Cell-Penetrating Peptide to Target Mammalian Sperm in vitro

Barkalina, N., Jones, C., Townley, H. E., & Coward, K. (2015) · Nanomedicine · doi:10.2217/nnm.14.235 · Cited by 39

Development of novel broad-spectrum antimicrobial lipopeptides derived from plantaricin NC8 β

Wiman, E., Zattarin, E., Aili, D., Bengtsson, T., Selegård, R., & Khalaf, H. (2023) · Scientific Reports · doi:10.1038/s41598-023-31185-8 · Cited by 36

RepTB: a gene ontology based drug repurposing approach for tuberculosis

Passi, A., Rajput, N. K., Wild, D. J., & Bhardwaj, A. (2018) · Journal of Cheminformatics · doi:10.1186/s13321-018-0276-9 · Cited by 36

Mitigation of heterocyclic aromatic amines in cooked meat. Part I: Informed selection of antioxidants based on molecular modeling

Meurillon, M., Angénieux, M., Mercier, F., Blinet, P., Chaloin, L., Chevolleau, S., Debrauwer, L., & Engel, E. (2020) · Food Chemistry · doi:10.1016/j.foodchem.2020.127264 · Cited by 33

Synthesis and biological evaluation of a library of hybrid derivatives as inhibitors of influenza virus PA-PB1 interaction

D’Agostino, I., Giacchello, I., Nannetti, G., Fallacara, A. L., Deodato, D., Musumeci, F., Grossi, G., Palù, G., Cau, Y., Trist, I. M. L., et al. (2018) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.08.032 · Cited by 33

“Pinning strategy”: a novel approach for predicting the backbone structure in terms of protein blocks from sequence

de Brevern, A. G., Etchebest, C., Benros, C., & Hazout, S. (2007) · Journal of Biosciences · doi:10.1007/s12038-007-0006-3 · Cited by 31

Highly Efficient Deamidation of Wheat Gluten by Glucose-Citric Acid-Based Natural Deep Eutectic Solvent: A Potential Effective Reaction Media

Cao, S., Zheng, W., Chen, Z.-P., Zhang, F.-L., Jiang, W., Qiu, Y.-Q., Gu, M., Chen, Z., Zheng, T., Zhang, H., et al. (2021) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c07275 · Cited by 30

Combined in silico approaches for the identification of novel inhibitors of human islet amyloid polypeptide (hIAPP) fibrillation

Patel, P. N., Parmar, K., Vyas, V. K., Patel, D., & Das, M. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.09.004 · Cited by 28

Matrix Metalloproteinase Responsive Delivery of Myostatin Inhibitors

Braun, A. C., Gutmann, M., Ebert, R., Jakob, F. J., Gieseler, H., Lühmann, T. C., & Meinel, L. (2016) · Pharmaceutical Research · doi:10.1007/s11095-016-2038-6 · Cited by 28

Prediction and Characterization of Cationic Arginine-Rich Plant Antimicrobial Peptide SM-985 From Teosinte (Zea mays ssp. mexicana)

Qutb, A. M., Wei, F., & Dong, W. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01353 · Cited by 27

SPROUTS: a database for the evaluation of protein stability upon point mutation

Lonquety, M., Lacroix, Z., Papandreou, N. C., & Chomilier, J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn704 · Cited by 26

Charge Distribution Fine-Tunes the Translocation of α -Helical Amphipathic Peptides across Membranes

Ablan, F. D. O., Spaller, B. L., Abdo, K. I., & Almeida, P. F. F. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.08.047 · Cited by 24

Surface‐Binding Peptide Facilitates Electricity‐Driven NADPH‐Free Cytochrome P450 Catalysis

Zernia, S., Frank, R., Weiße, R. H. ‐., Jahnke, H., Bellmann‐Sickert, K., Prager, A., Abel, B., Sträter, N., Robitzki, A. A., & Beck‐Sickinger, A. G. (2017) · ChemCatChem · doi:10.1002/cctc.201701810 · Cited by 24

In SilicoADME/Tox Predictions

Lagorce, D., Reynès, C., Camproux, A., Miteva, M. A., Spérandio, O., & Villoutreix, B. O. (2010) · Wiley eBooks · doi:10.1002/9780470915110.ch2 · Cited by 25

A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

Lagarde, N., Goldwaser, E., Pencheva, T., Jereva, D., Pajeva, I. K., Rey, J., Tufféry, P., Villoutreix, B. O., & Miteva, M. A. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184648 · Cited by 23

Experimental and Molecular Docking Studies of Cyclic Diphenyl Phosphonates as DNA Gyrase Inhibitors for Fluoroquinolone-Resistant Pathogens

Saleh, N. M., Moemen, Y. S., Mohamed, S., Fathy, G., Ahmed, A. A., Al‐Ghamdi, A. A., Ullah, S., & Sayed, I. E. T. E. (2022) · Antibiotics · doi:10.3390/antibiotics11010053 · Cited by 22

Structural effects of point mutations in proteins

Shanthirabalan, S., Chomilier, J., & Carpentier, M. (2018) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25499 · Cited by 24

Theoretical Insights into the Interactions between Star-Shaped Antimicrobial Polypeptides and Bacterial Membranes

Zhang, Y., Chen, T., Pan, Z., Sun, X., Yin, X., He, M., Xiao, S., & Liang, H. (2018) · Langmuir · doi:10.1021/acs.langmuir.8b02677 · Cited by 22

In silico docking studies of non-azadirachtin limonoids against ecdysone receptor of Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae)

Yadav, R. P., Ibrahim, K. S., Gurusubramanian, G., & Kumar, N. S. (2015) · Medicinal Chemistry Research · doi:10.1007/s00044-015-1320-1 · Cited by 21

Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology: Algorithms and Software Tools

Hamid, A. R., & Tran, Q. N. (2015) · Cited by 20

Probing the binding selected metal ions and biologically active substances to the antimicrobial peptide LL-37 using DSC, ITC measurements and calculations

Makowska, J., Wyrzykowski, D., Kamysz, E., Tesmar, A., Kamysz, W., & Chmurzyński, L. (2019) · Journal of Thermal Analysis and Calorimetry · doi:10.1007/s10973-019-08310-9 · Cited by 19

Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides

Hasegawa, K., Moriwaki, Y., Terada, T., Wei, C., & Shimizu, K. (2022) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720022500263 · Cited by 17

Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders

Aprahamian, M. L., Tikunova, S. B., Price, M. V., Cuesta, A. F., Davis, J. P., & Lindert, S. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00536 · Cited by 17

Broad-Spectrum Small-Molecule Inhibitors Targeting the SAM-Binding Site of Flavivirus NS5 Methyltransferase

Samrat, S. K., Bashir, Q., Huang, Y., Trieshmann, C. W., Tharappel, A. M., Zhang, R., Chen, K., Zheng, Y. G., Li, Z., & Li, H. (2023) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.2c00571 · Cited by 16

Site-Specific Conjugated Insulin-like Growth Factor-I for Anabolic Therapy

Wu, F., Braun, A. C., Lühmann, T. C., & Meinel, L. (2018) · ACS Biomaterials Science & Engineering · doi:10.1021/acsbiomaterials.7b01016 · Cited by 15

Marked difference in cytochrome c oxidation mediated by HO· and/or O2·− free radicals in vitro

Thariat, J., Collin, F., Marchetti, C., Sidahmed‐Adrar, N., Vitrac, H., Jore, D., & Gardès-Albert, M. (2008) · Biochimie · doi:10.1016/j.biochi.2008.04.018 · Cited by 15

In silico local structure approach: A case study on Outer Membrane Proteins

Martin, J., de Brevern, A. G., & Camproux, A. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21659 · Cited by 15

In silico approaches which are used in pharmacy

Al-Mohaya, M., Mesut, B., Kurt, A., & Çelik, Y. S. (2024) · Journal of Applied Pharmaceutical Science · doi:10.7324/japs.2024.154854 · Cited by 14

Designing a multi-epitope influenza vaccine: an immunoinformatics approach

Momajadi, L., Khanahmad, H., & Mahnam, K. (2024) · Scientific Reports · doi:10.1038/s41598-024-74438-w · Cited by 16

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Ahmad, H. I., Zhou, J., Ahmad, M. J., Afzal, G., Jiang, H., Zhang, X., Elokil, A., Khan, M. A., Li, L., Li, H., et al. (2020) · Aging · doi:10.18632/aging.102827 · Cited by 14

The Distribution of Standard Deviations Applied to High Throughput Screening

Hanley, Q. S. (2019) · Scientific Reports · doi:10.1038/s41598-018-36722-4 · Cited by 13

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

Lescat, M., Hoede, C., Clermont, O., Garry, L., Darlu, P., Tufféry, P., Denamur, É., & Picard, B. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-273 · Cited by 13

Pathogenic properties of Alzheimer's β-amyloid identified from structure–property patient-phenotype correlations

Tiwari, M. K., & Kepp, K. P. (2014) · Dalton Transactions · doi:10.1039/c4dt03122a · Cited by 12

Osteopontin induces osteogenic differentiation by human periodontal ligament cells via calcium binding domain–ALK‐1 interaction

Chaikiawkeaw, D., Khorattanakulchai, N., Nammultriputtar, K., Rattanapisit, K., Everts, V. E., Kubera, A., Phoolcharoen, W., & Pavasant, P. (2021) · Journal of Periodontology · doi:10.1002/jper.21-0184 · Cited by 12

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes

Martin, J., Regad, L., Etchebest, C., & Camproux, A. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22091 · Cited by 12

In Vitro and In Vivo Antibiotic Capacity of Two Host Defense Peptides

Arenas, I., Ibarra-Valencia, M. A., Santana, F. L., Villegas, E., Hancock, R. E. W., & Corzo, G. A. (2020) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00145-20 · Cited by 11

In Silico Identification of Potential Inhibitors of the Wnt Signaling Pathway in Human Breast Cancer

Pinto, I. A., & da Silveira, N. J. F. (2019) · Journal of Computational Biology · doi:10.1089/cmb.2019.0311 · Cited by 11

Antibodies reacting with JCPyV_VP2 _167-15mer as a novel serological marker for JC polyomavirus infection

Lagatie, O., Loy, T. V., Tritsmans, L., & Stuyver, L. J. (2014) · Virology Journal · doi:10.1186/1743-422x-11-174 · Cited by 11

Co-lethality studied as an asset against viral drug escape: the HIV protease case

Brouillet, S., Valère, T., Ollivier, E., Marsan, L., & Vanet, A. (2010) · Biology Direct · doi:10.1186/1745-6150-5-40 · Cited by 10

Tailoring Uptake Efficacy of HSV-1 gD Tailoring Uptake Efficacy of Hsv-1 GD Derived Carrier Peptides

Bősze, S. E., Zsila, F., Biri‐Kovács, B., Szeder, B., Májer, Z., Hudecz, F., & Uray, K. (2020) · Biomolecules · doi:10.3390/biom10050721 · Cited by 10

Computational Biology and Chemistry in MTi: Emphasis on the Prediction of Some ADMET Properties

Miteva, M. A., & Villoutreix, B. O. (2017) · Molecular Informatics · doi:10.1002/minf.201700008 · Cited by 9

A New Strategy to Reduce Influenza Escape: Detecting Therapeutic Targets Constituted of Invariance Groups

Lao, J., & Vanet, A. (2017) · Viruses · doi:10.3390/v9030038 · Cited by 8

EIF4A3 targeted therapeutic intervention in glioblastoma multiforme using phytochemicals from Indian medicinal plants – an integration of phytotherapy into precision onco-medicine

Kulavi, S., Dhar, D., Kamal, I. M., Chakrabarti, S., & Bandyopadhyay, J. (2024) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2024.2314257 · Cited by 7

Loop Simulations

Totrov, M. M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-588-6_9 · Cited by 7

DESP: Deep Enhanced Sampling of Proteins’ Conformation Spaces Using AI-Inspired Biasing Forces

Salawu, E. O. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.587151 · Cited by 7

Functional analysis of Escherichia coli K12 toxin-antitoxin systems as novel drug targets using a network biology approach

Shetty, S. C., Shastry, R. P., Shetty, V., Patil, P., Shetty, P. K., & Ghate, S. D. (2022) · Microbial Pathogenesis · doi:10.1016/j.micpath.2022.105683 · Cited by 6

Tools for Green Molecular Design to Reduce Toxicological Risk

Faulkner, D. M., Shen, L. K. R., Rosa, V. Y. D. L., Johnson, D. E., Hemingway, R., Williams, R. V., Judson, P. N., Arnold, J., & Vulpe, C. D. (2017) · Royal Society of Chemistry eBooks · doi:10.1039/9781782623731-00036 · Cited by 6

Beyond the venom: Exploring the antimicrobial peptides from Androctonus species of scorpion

Sujatha, V. A., Gopalakrishnan, C., Anbarasu, A., Ponnusamy, C. S., Choudhary, R., Geetha, S. A. S., & Rajasekaran, R. (2024) · Journal of Peptide Science · doi:10.1002/psc.3613 · Cited by 5

Protein intrachain contact prediction with most interacting residues (MIR)

Acuña, R., Lacroix, Z., Papandreou, N. C., & Chomilier, J. (2014) · Bio-Algorithms and Med-Systems · doi:10.1515/bams-2014-0015 · Cited by 5

Identification of new potent agonists for toll-like receptor 8 by virtual screening methods, molecular dynamics simulation, and MM-GBSA

Sadeghkhani, F., Hajihassan, Z., & Gharaghani, S. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2152368 · Cited by 5

Synthetic lethals in HIV: ways to avoid drug resistance

Petitjean, M., Badel, A., Veitia, R. A., & Vanet, A. (2015) · Biology Direct · doi:10.1186/s13062-015-0044-y · Cited by 5

Analyses of displacements resulting from a point mutation in proteins

Carpentier, M., & Chomilier, J. (2020) · Journal of Structural Biology · doi:10.1016/j.jsb.2020.107543 · Cited by 5

Phylogenetic, molecular evolution and structural analyses of the WFDC1/prostate stromal protein 20 (ps20)

Calero, C. S., & Carvalho, H. F. (2018) · Gene · doi:10.1016/j.gene.2018.10.046 · Cited by 5

Structure‐function relationship between a natural cosmetic active ingredient and the olfactory receptor OR2AT4

Verzeaux, L., Richer, S., Viguier, J., Gofflo, S., Boudier, D., Aymard, E., & Closs, B. (2019) · International Journal of Cosmetic Science · doi:10.1111/ics.12526 · Cited by 5

A Workflow Engine for the Execution of Scientific Protocols

Ménager, H., & Lacroix, Z. (2006) · IEEE International Conference on Data Engineering Workshops (ICDEW) · doi:10.1109/icdew.2006.24 · Cited by 5

In silico characterization of Leptospira interrogans DNA ligase A and delineation of its antimicrobial stretches

Mishra, P. K. K., & Nimmanapalli, R. (2019) · Annals of Microbiology · doi:10.1007/s13213-019-01516-0 · Cited by 4

Bioinformatics Applications Discovery and Composition with the Mobyle Suite and MobyleNet

Ménager, H., Gopalan, V., Néron, B., Larroudé, S., Maupetit, J., Saladin, A., Tufféry, P., Huyen, Y., & Caudron, B. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-27392-6_2 · Cited by 4

Molecular Dynamics of Membrane Peptides and Proteins: Principles and Comparison to Experimental Data

Fuchs, P. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-762-4_21 · Cited by 4

Identification of MHC Class I bound peptides of Francisella tularensis Live Vaccine Strain using mass spectrometry

Gaur, R., Verma, D. K., Alam, S. I., & Kamboj, D. V. (2020) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2020.105651 · Cited by 4

Side-chain modification of collagen-targeting peptide prevents dye aggregation for improved molecular imaging of arthritic joints

Michie, M. S., Xu, B. J., Sudlow, G. P., Springer, L. E., Pham, C. T. N., & Achilefu, S. A. (2021) · Journal of Photochemistry and Photobiology A Chemistry · doi:10.1016/j.jphotochem.2021.113624 · Cited by 4

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion

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Desmoplakin CSM models unravel mechanisms regulating the binding to intermediate filaments and putative therapeutics for cardiocutaneous diseases

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