Comparative modeling for protein structure prediction

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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Assessment of protein models with three-dimensional profiles

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Comparative Protein Structure Modeling of Genes and Genomes

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The relation between the divergence of sequence and structure in proteins.

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Recognition of errors in three‐dimensional structures of proteins

Sippl, M. J. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170404 · Cited by 2,156 · see citing works

Protein Structure Prediction and Structural Genomics

Baker, D., & Sali, A. (2001) · Science · doi:10.1126/science.1065659 · Cited by 1,587 · see citing works

Toward High-Resolution de Novo Structure Prediction for Small Proteins

Bradley, P. H., Misura, K. M. S., & Baker, D. A. (2005) · Science · doi:10.1126/science.1113801 · Cited by 865 · see citing works

3D-Jury: a simple approach to improve protein structure predictions

Ginalski, K., Elofsson, A., Fischer, D., & Rychlewski, L. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg124 · Cited by 719 · see citing works

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction

Moult, J. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.05.011 · Cited by 485 · see citing works

Fold Change in Evolution of Protein Structures

Grishin, N. V. (2001) · Journal of Structural Biology · doi:10.1006/jsbi.2001.4335 · Cited by 445 · see citing works

Automated structure prediction of weakly homologous proteins on a genomic scale

Zhang, Y., & Skolnick, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0305695101 · Cited by 344 · see citing works

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

Deshpande, N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki057 · Cited by 341 · see citing works

Modeling structurally variable regions in homologous proteins with rosetta

Rohl, C. A., Strauss, C. E. M., Chivian, D. C., & Baker, D. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10629 · Cited by 321 · see citing works

Protein structure modeling for structural genomics.

Sánchez, R., Pieper, U., Melo, F., Eswar, N., Martı́-Renom, M. A., Madhusudhan, M. S., Mirković, N., & Šali, A. (2000) · Nature Structural Biology · doi:10.1038/80776 · Cited by 216 · see citing works

Structure prediction meta server

Bujnicki, J. M., Elofsson, A., Fischer, D., & Rychlewski, L. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.750 · Cited by 206 · see citing works

CAFASP2: The second critical assessment of fully automated structure prediction methods

Fischer, D., Elofsson, A., Rychlewski, L., Pazos, F., Valencia, A., Rost, B., Ortíz, Á. R., & Dunbrack, R. L. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10036 · Cited by 198 · see citing works

Progress over the first decade of CASP experiments

Kryshtafovych, A., Venclovas, Č., Fidelis, K. A., & Moult, J. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20740 · Cited by 179 · see citing works

Critical assessment of methods of protein structure prediction (CASP)—Round 6

Moult, J., Fidelis, K. A., Rost, B., Hubbard, T., & Tramontano, A. L. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20716 · Cited by 179 · see citing works

EVA: evaluation of protein structure prediction servers

Koh, I. Y. Y. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg619 · Cited by 168 · see citing works

3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor

Fischer, D. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10357 · Cited by 161 · see citing works

Evolution of protein structures and functions

Kinch, L. N., & Grishin, N. V. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00338-x · Cited by 160 · see citing works

Progress and challenges in high‐resolution refinement of protein structure models

Misura, K. M. S., & Baker, D. A. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20376 · Cited by 153 · see citing works

Scoring profile‐to‐profile sequence alignments

Wang, G., & Dunbrack, R. L. (2004) · Protein Science · doi:10.1110/ps.03601504 · Cited by 135 · see citing works

Practical lessons from protein structure prediction

Ginalski, K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki327 · Cited by 124 · see citing works

Assessment of predictions submitted for the CASP6 comparative modeling category

Tress, M. L., Ezkurdia, I., Graña‐Castro, O., López, G., & Valencia, A. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20720 · Cited by 119 · see citing works

LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction

Rychlewski, L., & Fischer, D. (2004) · Protein Science · doi:10.1110/ps.04888805 · Cited by 104 · see citing works

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models

Koliński, A., & Bujnicki, J. M. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20723 · Cited by 103 · see citing works

Profile–profile methods provide improved fold‐recognition: A study of different profile–profile alignment methods

Ohlson, T., Wallner, B., & Elofsson, A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20184 · Cited by 98 · see citing works

CAFASP3: The third critical assessment of fully automated structure prediction methods

Fischer, D., Rychlewski, L., Dunbrack, R. L., Ortíz, Á. R., & Elofsson, A. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10538 · Cited by 95 · see citing works

Detecting distant homology with Meta-BASIC

Ginalski, K., von Grotthuss, M., Grishin, N. V., & Rychlewski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh370 · Cited by 94 · see citing works

Progress towards mapping the universe of protein folds.

Grant, A., Lee, D. K., & Orengo, C. A. (2004) · Genome biology · doi:10.1186/gb-2004-5-5-107 · Cited by 81 · see citing works

Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment

Venclovas, Č., & Margelevičius, M. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20725 · Cited by 75 · see citing works

SPARKS 2 and SP3 servers in CASP6

Zhou, H., & Zhou, Y. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20732 · Cited by 72 · see citing works

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment

Ginalski, K., & Rychlewski, L. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10548 · Cited by 69 · see citing works

Accuracy of structure-derived properties in simple comparative models of protein structures

Chakravarty, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki162 · Cited by 66 · see citing works

Evaluating the usefulness of protein structure models for molecular replacement

Giorgetti, A., Raimondo, D., Miele, A. E., & Tramontano, A. L. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1112 · Cited by 66 · see citing works

Automatic target selection for structural genomics on eukaryotes

Liu, J., Hegyi, H., Acton, T., Montelione, G. T., & Rost, B. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20012 · Cited by 66 · see citing works

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation

Qian, B., Ortíz, Á. R., & Baker, D. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404703101 · Cited by 62 · see citing works

Improving Fold Recognition Without Folds

Przybylski, D., & Rost, B. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.05.041 · Cited by 54 · see citing works

Relationship between multiple sequence alignments and quality of protein comparative models

Cozzetto, D., & Tramontano, A. L. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20284 · Cited by 51 · see citing works

Molecular modeling of protein function regions

DeWeese-Scott, C., & Moult, J. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10519 · Cited by 44 · see citing works

PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

Margelevičius, M., & Venclovas, Č. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-185 · Cited by 35 · see citing works

Gaps in structurally similar proteins: Towards improvement of multiple sequence alignment

Wrabl, J. O., & Grishin, N. V. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10508 · Cited by 34 · see citing works

Protein Family Clustering for Structural Genomics

Yan, Y., & Moult, J. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.08.058 · Cited by 30 · see citing works

Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs

Sadreyev, R. I., & Grishin, N. V. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg485 · Cited by 27 · see citing works

Empirical limits for template‐based protein structure prediction: the CASP5 example

Contreras‐Moreira, B., Ezkurdia, I., Tress, M. L., & Valencia, A. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.01.014 · Cited by 21 · see citing works

Systematic Analysis of Added-Value in Simple Comparative Models of Protein Structure

Chakravarty, S., & Sánchez, R. (2004) · Structure · doi:10.1016/j.str.2004.05.018 · Cited by 20 · see citing works

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

Wiederstein, M., & Sippl, M. J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm290 · Cited by 5,909 · see citing works

Protein Structure Modeling with MODELLER

Eswar, N., Eramian, D., Webb, B., Shen, M., & Šali, A. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-058-8_8 · Cited by 1,781 · see citing works

Protein Structure Modeling with MODELLER

Webb, B., & Šali, A. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0366-5_1 · Cited by 600 · see citing works

Homology modeling in drug discovery: current trends and applications

Cavasotto, C. N., & Phatak, S. S. (2009) · Drug Discovery Today · doi:10.1016/j.drudis.2009.04.006 · Cited by 484 · see citing works

Ion mobility mass spectrometry of proteins and proteinassemblies

Uetrecht, C., Rose, R., van Duijn, E., Lorenzen, K., & Heck, A. J. R. (2009) · Chemical Society Reviews · doi:10.1039/b914002f · Cited by 460 · see citing works

Protein Structure Modeling with MODELLER

Webb, B., & Šali, A. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7231-9_4 · Cited by 416 · see citing works

Substrate specificity of plant UDP-dependent glycosyltransferases predicted from crystal structures and homology modeling

Osmani, S. A., Bak, S., & Møller, B. L. (2009) · Phytochemistry · doi:10.1016/j.phytochem.2008.12.009 · Cited by 283 · see citing works

Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications

Liu, X. R., Zhang, M. M., & Gross, M. L. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00815 · Cited by 241 · see citing works

The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development

Gray, R. S., Abitua, P. B., Wlodarczyk, B. J., Szabo‐Rogers, H. L., Blanchard, O., Lee, I., Weiss, G. S., Liu, K. J., Marcotte, E. M., Wallingford, J. B., et al. (2009) · Nature Cell Biology · doi:10.1038/ncb1966 · Cited by 220 · see citing works

The implications of alternative splicing in the ENCODE protein complement

Tress, M. L., Martelli, P. L., Frankish, A., Reeves, G. A., Wesselink, J., Yeats, C., Olason, P., Albrecht, M., Hegyi, H., Giorgetti, A., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700800104 · Cited by 222 · see citing works

Structural and Functional Analysis of SGT1 Reveals That Its Interaction with HSP90 Is Required for the Accumulation of Rx, an R Protein Involved in Plant Immunity

Botër, M., Amigues, B., Peart, J. R., Breuer, C., Kadota, Y., Casais, C., Moore, G. R., Kleanthous, C., Ochsenbein, F., Shirasu, K., et al. (2007) · The Plant Cell · doi:10.1105/tpc.107.050427 · Cited by 204 · see citing works

Protein Structure Modeling with MODELLER

Webb, B., & Šali, A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0892-0_14 · Cited by 210 · see citing works

Acyltransferases in Bacteria

Röttig, A., & Steinbüchel, A. (2013) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00010-13 · Cited by 169 · see citing works

Template-based structure modeling of protein–protein interactions

Szilágyi, A., & Zhang, Y. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.11.005 · Cited by 168 · see citing works

Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening

Cavasotto, C. N., Orry, A. J. W., Murgolo, N., Czarniecki, M., Kocsi, S. A., Hawes, B. E., O’Neill, K. A., Hine, H., Burton, M. S., Voigt, J. H., et al. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm070759m · Cited by 167 · see citing works

Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics

Klebba, P. E., Newton, S. M. C., Six, D. A., Kumar, A., Yang, T., Nairn, B. L., Munger, C., & Chakravorty, S. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01005 · Cited by 150 · see citing works

Dopamine D1receptor ligands: Where are we now and where are we going

Zhang, J., Xiong, B., Zhen, X., & Zhang, A. (2008) · Medicinal Research Reviews · doi:10.1002/med.20130 · Cited by 145 · see citing works

Structure-based drug repurposing: Traditional and advanced AI/ML-aided methods

Choudhury, C., Murugan, N. A., & Priyakumar, U. D. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.03.006 · Cited by 136 · see citing works

Comparative Protein Structure Modelling

Fiser, A. (2008) · Springer eBooks · doi:10.1007/978-1-4020-9058-5_3 · Cited by 133 · see citing works

High-resolution design of a protein loop

Hu, X., Wang, H., Ke, H., & Kuhlman, B. A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707977104 · Cited by 126 · see citing works

Computational methods in protein structure prediction

Floudas, C. A. (2007) · Biotechnology and Bioengineering · doi:10.1002/bit.21411 · Cited by 116 · see citing works

COMPUTATIONAL ENZYME DESIGN APPROACHES WITH SIGNIFICANT BIOLOGICAL OUTCOMES: PROGRESS AND CHALLENGES

Li, X., Zhang, Z., & Song, J. (2012) · Computational and Structural Biotechnology Journal · doi:10.5936/csbj.201209007 · Cited by 111 · see citing works

Fold assessment for comparative protein structure modeling

Melo, F., & Šali, A. (2007) · Protein Science · doi:10.1110/ps.072895107 · Cited by 105 · see citing works

Intrarenal 1-methoxypyrene, an aryl hydrocarbon receptor agonist, mediates progressive tubulointerstitial fibrosis in mice

Cao, G., Miao, H., Wang, Y., Chen, D., Wu, X., Chen, L., Guo, Y. P., Zou, L., Vaziri, N. D., Li, P., et al. (2022) · Acta Pharmacologica Sinica · doi:10.1038/s41401-022-00914-6 · Cited by 109 · see citing works

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

Garzón, J. I., Kovacs, J., Abagyan, R. A., & Chacón, P. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl625 · Cited by 103 · see citing works

Protein structure prediction and model quality assessment

Kryshtafovych, A., & Fidelis, K. A. (2009) · Drug Discovery Today · doi:10.1016/j.drudis.2008.11.010 · Cited by 99 · see citing works

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences

Mizianty, M. J., & Kurgan, L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-414 · Cited by 96 · see citing works

Analyzing Protein Interaction Networks Using Structural Information

Kiel, C., Beltrão, P., & Serrano, L. G. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.062706.133317 · Cited by 85 · see citing works

Structural Models of Human eEF1A1 and eEF1A2 Reveal Two Distinct Surface Clusters of Sequence Variation and Potential Differences in Phosphorylation

Soares, D. C., Barlow, P. N., Newbery, H. J., Porteous, D. J., & Abbott, C. M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006315 · Cited by 85 · see citing works

The Capsid of the T4 Phage Superfamily: The Evolution, Diversity, and Structure of Some of the Most Prevalent Proteins in the Biosphere

Comeau, A., & Krisch, H. M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn080 · Cited by 84 · see citing works

Molecular Modeling and Ligand Docking for Solute Carrier (SLC) Transporters

Schlessinger, A., Khuri, N., Giacomini, K. M., & Šali, A. (2013) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026611313070007 · Cited by 83 · see citing works

Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA

Andersen, P., Nielsen, M. A., Resende, M., Rask, T. S., Dahlbäck, M., Theander, T., Lund, O., & Salanti, A. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.0040042 · Cited by 79 · see citing works

Aqueous phase polymeric corrosion inhibitors: Recent advancements and future opportunities

Verma, C., Quraishi, M. A., & Rhee, K. Y. (2021) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2021.118387 · Cited by 81 · see citing works

Refining homology models by combining replica‐exchange molecular dynamics and statistical potentials

Zhu, J., Fan, H., Périole, X., Honig, B. H., & Mark, A. E. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22005 · Cited by 79 · see citing works

Evolutionary constraints on structural similarity in orthologs and paralogs

Peterson, M. E., Chen, F., Saven, J. G., Roos, D. S., Babbitt, P. C., & Šali, A. (2009) · Protein Science · doi:10.1002/pro.143 · Cited by 79 · see citing works

Identification of endogenous 1‐aminopyrene as a novel mediator of progressive chronic kidney disease via aryl hydrocarbon receptor activation

Miao, H., Cao, G., Wu, X., Chen, Y., Chen, D., Chen, L., Vaziri, N. D., Feng, Y., Su, W. C., Gao, Y. G., et al. (2020) · British Journal of Pharmacology · doi:10.1111/bph.15062 · Cited by 80 · see citing works

Computational tools for epitope vaccine design and evaluation

He, L., & Zhu, J. (2015) · Current Opinion in Virology · doi:10.1016/j.coviro.2015.03.013 · Cited by 75 · see citing works

Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation

Shahlaei, M., Madadkar‐Sobhani, A., Mahnam, K., Fassihi, A., Saghaie, L., & Mansourian, M. (2010) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2010.12.004 · Cited by 74 · see citing works

Ligand binding and homology modelling of insect odorant‐binding proteins

Venthur, H., Mutis, A., Zhou, J., & Quiróz, A. (2014) · Physiological Entomology · doi:10.1111/phen.12066 · Cited by 72 · see citing works

Origin of an ancient hormone/receptor couple revealed by resurrection of an ancestral estrogen

Markov, G. V., Gutierrez-Mazariegos, J., Pitrat, D., Billas, I. M. L., Bonneton, F., Moras, D., Hasserodt, J., Lecointre, G., & Laudet, V. (2017) · Science Advances · doi:10.1126/sciadv.1601778 · Cited by 72 · see citing works

Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: Application to galectin-1

Charvátová, O., Foley, B. L., Bern, M. W., Sharp, J. S., Orlando, R., & Woods, R. J. (2008) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2008.07.013 · Cited by 71 · see citing works

Homology modeling of human Toll‐like receptors TLR7, 8, and 9 ligand‐binding domains

Wei, T., Gong, J., Jamitzky, F., Heckl, W. M., Stark, R. W., & Rössle, S. C. (2009) · Protein Science · doi:10.1002/pro.186 · Cited by 65 · see citing works

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments

Baeten, L., Reumers, J., Tur, V., Stricher, F., Lenaerts, T., Serrano, L. G., Rousseau, F., & Schymkowitz, J. W. H. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000083 · Cited by 64 · see citing works

High incidence of ubiquitin‐like domains in human ubiquitin‐specific proteases

Zhu, X., Menard, R., & Sulea, T. I. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21546 · Cited by 64 · see citing works

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

Felts, A. K., Gallicchio, E., Chekmarev, D. S., Paris, K. A., Friesner, R. A., & Levy, R. M. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct800051k · Cited by 63 · see citing works

Mutations as trapdoors to two competing native conformations of the Rop-dimer

Schug, A. H., Whitford, P. C., Levy, Y., & Onuchic, J. N. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706077104 · Cited by 63 · see citing works

An extracellular lipase from Amycolatopsis mediterannei is a cutinase with plastic degrading activity

Tan, Y., HENEHAN, G. T. M., Kinsella, G. K., & Ryan, B. J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.019 · Cited by 62 · see citing works

Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures

Beuming, T., Martín, H., Díaz-Rovira, A. M., Díaz, L., Guallar, V., & Ray, S. S. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00796 · Cited by 61 · see citing works

Quality assessment of protein model-structures using evolutionary conservation

Kalman, M., & Ben‐Tal, N. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq114 · Cited by 55 · see citing works

Structural Similarity between the Prion Domain of HET-s and a Homologue Can Explain Amyloid Cross-Seeding in Spite of Limited Sequence Identity

Wasmer, C., Zimmer, A., Sabaté, R., Soragni, A., Saupe, S. J., Ritter, C., & Meier, B. H. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.06.053 · Cited by 53 · see citing works

A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction

Nikolaev, D. M., Shtyrov, A. A., Panov, M. S., Jamal, A., Chakchir, O. B., Kochemirovsky, V. A., Olivucci, M., & Ryazantsev, M. N. (2018) · ACS Omega · doi:10.1021/acsomega.8b00721 · Cited by 53 · see citing works

Metagenomic gene discovery: How far have we moved into novel sequence space?

Tuffin, M. I., Anderson, D. E., Heath, C., & Cowan, D. A. (2009) · Biotechnology Journal · doi:10.1002/biot.200900235 · Cited by 52 · see citing works

Structural Characterization of Open Reading Frame-Encoded Functional Genes from Tilapia Lake Virus (TiLV)

Acharya, V., Chakraborty, H. J., Rout, A. K., Balabantaray, S., Behera, B. K., & Das, B. K. (2019) · Molecular Biotechnology · doi:10.1007/s12033-019-00217-y · Cited by 52 · see citing works

Sortase independent and dependent systems for acquisition of haem and haemoglobin in <i>Listeria monocytogenes</i>

Xiao, Q., Jiang, X., Moore, K. J., Shao, Y., Pi, H., Dubail, I., Charbit, A., Newton, S. M., & Klebba, P. E. (2011) · Molecular Microbiology · doi:10.1111/j.1365-2958.2011.07667.x · Cited by 51 · see citing works

A novel structure-based virtual screening model for the hERG channel blockers

Du, L., Li, M., You, Q., & Xia, L. H. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.02.068 · Cited by 50 · see citing works

TonB-Dependent Heme/Hemoglobin Utilization by Caulobacter crescentus HutA

Balhesteros, H., Shipelskiy, Y., Long, N. J., Majumdar, A., Katz, B. B., dos Santos, N. M., Leaden, L., Newton, S. M. C., Marques, M. V., & Klebba, P. E. (2016) · Journal of Bacteriology · doi:10.1128/jb.00723-16 · Cited by 48 · see citing works

Survey of Similarity-Based Prediction of Drug-Protein Interactions

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Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain

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