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

The protein data bank: A computer-based archival file for macromolecular structures

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574

The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution

Fermi, G., Perutz, M. F., Shaanan, B., & Fourme, R. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90472-8 · Cited by 770

The Protein Data Bank

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., RODGERS, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1977.tb11885.x · Cited by 763

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., & Kraut, J. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)33497-5 · Cited by 746

How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins

Lesk, A. M., & Chothia, C. (1980) · Journal of Molecular Biology · doi:10.1016/0022-2836(80)90373-3 · Cited by 712

Structure and refinement of oxymyoglobin at 1·6 Å resolution

Phillips, S. E. V. (1980) · Journal of Molecular Biology · doi:10.1016/0022-2836(80)90262-4 · Cited by 643

Conformation change of cytochrome c

Takano, T., & Dickerson, R. E. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90529-5 · Cited by 557

Structure of oxidized poplar plastocyanin at 1·6 Å resolution

Guss, J. M., & Freeman, H. C. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80064-3 · Cited by 507

Structure of bovine pancreatic trypsin inhibitor

Wlodawer, A., WALTER, J., Huber, R., & Sjölin, L. (1984) · Journal of Molecular Biology · doi:10.1016/s0022-2836(84)80006-6 · Cited by 478

Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.9 Å resolution

Marquart, M., Deisenhofer, J., Huber, R., & Palm, W. (1980) · Journal of Molecular Biology · doi:10.1016/0022-2836(80)90252-1 · Cited by 457

Statistical potential‐based amino acid similarity matrices for aligning distantly related protein sequences

Tan, Y. H., Huang, H., & Kihara, D. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21020 · Cited by 41

Simultaneous Bayesian Estimation of Alignment and Phylogeny under a Joint Model of Protein Sequence and Structure

Herman, J. L., Challis, C. J., Novák, Á., Hein, J., & Schmidler, S. C. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu184 · Cited by 42

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

Terwilliger, T. C., Read, R. J., Adams, P. D., Brünger, A. T., Afonine, P. V., Grosse‐Kunstleve, R. W., & Hung, L. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444912015636 · Cited by 42

High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2)

Hayes, M. L., Eytan, R. I., & Hellberg, M. E. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-150 · Cited by 43

Probing the Structure of Hirudin from Hirudinaria manillensis by Limited Proteolysis

Vindigni, A., Filippis, V. D., Zanotti, G., Visco, C., Orsini, G., & Fontana, A. (1994) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1994.tb20056.x · Cited by 41

Genetic Selection for Critical Residues in Ribonucleases

Smith, B. D., & Raines, R. T. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.07.020 · Cited by 41

The Effect of Sequence Evolution on Protein Structural Divergence

Williams, S. G., & Lovell, S. C. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp020 · Cited by 41

Reconstitution of cyanogenesis in barley (Hordeum vulgare L.) and its implications for resistance against the barley powdery mildew fungus

Nielsen, K. A., Hrmová, M., Nielsen, J. N., Forslund, K., Ebert, S., Olsen, C. E., Fincher, G. B., & Møller, B. L. (2005) · Planta · doi:10.1007/s00425-005-0158-z · Cited by 41

Spinach CSP41, an mRNA-Binding Protein and Ribonuclease, Is Homologous to Nucleotide-Sugar Epimerases and Hydroxysteroid Dehydrogenases

Baker, M. E., Grundy, W. N., & Elkan, C. (1998) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1998.8951 · Cited by 41

A ribosomal protein module in EF-G and DNA gyrase

Murzin, A. G. (1995) · Nature Structural Biology · doi:10.1038/nsb0195-25 · Cited by 41

Crystal structure of theTrypanosoma cruzi trypanothione reductase·mepacrine complex

Jacoby, E. M. T., Schlichting, I., Lantwin, C. B., Kabsch, W., & Krauth‐Siegel, R. L. (1996) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199601)24:1 · Cited by 112

Inferring Evolution of Fish Proteins: The Globin Case Study

Dettaı̈, A., di Prisco, G., Lecointre, G., Parisi, E., & Verde, C. (2008) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(08)36030-3 · Cited by 41

An Assessment of the Impacts of Molecular Oxygen on the Evolution of Proteomes

Vieira‐Silva, S., & Rocha, E. P. C. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn142 · Cited by 40

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells

Nasir, A., Kim, K. M., & Caetano‐Anollés, G. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01178 · Cited by 40

Molecular function limits divergent protein evolution on planetary timescales

Konaté, M. M., Plata, G., Park, J., Usmanova, D. R., Wang, H. H., & Vitkup, D. (2019) · eLife · doi:10.7554/elife.39705 · Cited by 39

Structure Unveils Relationships between RNA Virus Polymerases

Mönttinen, H. A. M., Ravantti, J., & Poranen, M. M. (2021) · Viruses · doi:10.3390/v13020313 · Cited by 40

Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

Panjkovich, A., & Daura, X. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-9 · Cited by 42

Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison

Green, R. E., & Brenner, S. E. (2002) · Proceedings of the IEEE · doi:10.1109/jproc.2002.805303 · Cited by 40

Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases

Mathura, V. S., Schein, C. H., & Braun, W. A. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg164 · Cited by 40

Ligand induced conformational states of the 5-HT1A receptor

Sylte, I., Bronowska, A. K., & Dahl, S. G. (2001) · European Journal of Pharmacology · doi:10.1016/s0014-2999(01)00860-3 · Cited by 40

Data mining the protein data bank: Residue interactions

Oldfield, T. J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10221 · Cited by 40

Post-genomic science: converting primary structure into physiological function

Benner, S. A., Trabesinger-Rüf, N., & Schreiber, D. (1998) · Advances in Enzyme Regulation · doi:10.1016/s0065-2571(97)00019-8 · Cited by 40

Different protein sequences can give rise to highly similar folds through different stabilizing interactions

Laurents, D. V., Subbiah, S., & Levitt, M. (1994) · Protein Science · doi:10.1002/pro.5560031105 · Cited by 40

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Iantorno, S. A., Gori, K. C., Goldman, N., Gil, M., & Dessimoz, C. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_4 · Cited by 39

Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships

Jianhong, Z., Oldfield, C. J., Yan, W., Shen, B., & Dunker, A. K. (2019) · Protein Science · doi:10.1002/pro.3680 · Cited by 40

Computational predictive approaches for interaction and structure of aptamers

Emami, N., Pakchin, P. S., & Ferdousi, R. (2020) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2020.110268 · Cited by 40

Cloning and homology modelling of a Pto-like protein kinase family of common bean (Phaseolus vulgaris L.)

Vallad, G. E., Rivkin, M. I., Vallejos, C. E., & McClean, P. E. (2001) · Theoretical and Applied Genetics · doi:10.1007/s001220100705 · Cited by 39

Comparison of sequence and structure alignments for protein domains

Marchler‐Bauer, A., Panchenko, A. R., Ariel, N., & Bryant, S. H. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10163 · Cited by 39

Conformational substates in different crystal forms of the photoactive yellow protein—Correlation with theoretical and experimental flexibility

van Aalten, D. M. F., Joshua‐Tor, L., Wim Crielaard, A., & Hellingwerf, K. J. (2000) · Protein Science · doi:10.1110/ps.9.1.64 · Cited by 39

Structural and functional organization of the peripheral light-harvesting system in Photosystem I

Melkozernov, A. N., & Blankenship, R. E. (2005) · Photosynthesis Research · doi:10.1007/s11120-004-6474-5 · Cited by 39

Classification of proteins based on the properties of the ligand‐binding site: The case of adenine‐binding proteins

Cappello, V., Tramontano, A. L., & Koch, U. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10070 · Cited by 39

A new approach to the study of haematopoietic development in the yolk sac and embryoid bodies

Guimarães, M. J., Bazán, J. F., Zlotnik, A., Wiles, M. V., Grimaldi, J. C., Lee, F., & McClanahan, T. K. (1995) · Development · doi:10.1242/dev.121.10.3335 · Cited by 39

The PB1 domain and the PC motif‐containing region are structurally similar protein binding modules

Yoshinaga, S., Kohjima, M., Ogura, K., Yokochi, M., Takeya, R., Ito, T., Sumimoto, H., & Inagaki, F. (2003) · EMBO Journal · doi:10.1093/emboj/cdg475 · Cited by 40

Molecular replacement: tricks and treats

Abergel, C. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913015291 · Cited by 36

Conformational diversity and the emergence of sequence signatures during evolution

Parisi, G. D., Zea, D. J., Monzón, A. M., & Marino‐Buslje, C. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.02.005 · Cited by 42

Chemical Fragments that Hydrogen Bond to Asp, Glu, Arg, and His Side Chains in Protein Binding Sites

Chan, A. W. E., Laskowski, R. A., & Selwood, D. L. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm901696w · Cited by 38

Amino Acid Preferences for a Critical Substrate Binding Subsite of Retroviral Proteases in Type 1 Cleavage Sites

Bagossi, P., Sperka, T., Fehér, A., Kádas, J., Zahuczky, G., Miklóssy, G., Boross, P., & Tőzsér, J. (2005) · Journal of Virology · doi:10.1128/jvi.79.7.4213-4218.2005 · Cited by 38

Prevalence and phylogenetic analysis of tick-borne encephalitis virus (TBEV) in field-collected ticks (Ixodes ricinus) in southern Switzerland

Rieille, N., Bressanelli, S., Freire, C. C. D. M., Arcioni, S., Gern, L., Péter, O., & Voordouw, M. J. (2014) · Parasites & Vectors · doi:10.1186/1756-3305-7-443 · Cited by 38

Engineering Protein Sequence Composition for Folding Robustness Renders Efficient Noncanonical Amino acid Incorporations

Soundrarajan, N., Merkel, L., Budiša, N., Raghunathan, G., Ayyadurai, N., Sriram, S., Yun, H., & Lee, S. (2010) · ChemBioChem · doi:10.1002/cbic.201000380 · Cited by 38

Structural and molecular aspects of betaine-GABA transporter 1 (BGT1) and its relation to brain function

Kickinger, S., Hellsberg, E., Frølund, B., Schousboe, A., Ecker, G. F., & Wellendorph, P. (2019) · Neuropharmacology · doi:10.1016/j.neuropharm.2019.05.021 · Cited by 38

Modulation of the expression of ryanodine receptor mRNA from Plutella xylostella as a result of diamide insecticide application

Sun, L., Cui, L., Rui, C., Yan, X., Yang, D., & Yuan, H. (2012) · Gene · doi:10.1016/j.gene.2012.09.027 · Cited by 37

The insect immune protein scolexin is a novel serine proteinase homolog

Finnerty, C. M., Granados, R. R., & Karplus, P. A. (1999) · Protein Science · doi:10.1110/ps.8.1.242 · Cited by 38

Molecular Properties of 5‐Hydroxytryptamine3 Receptor‐Type Binding Sites Purified from NG1O8‐15 Cells

Boess, F., Lummis, S. C. R., & Martin, I. L. (1992) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.1992.tb11000.x · Cited by 38

Secondary structural predictions for the clostridial neurotoxins

Lebeda, F. J., & Olson, M. A. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340200402 · Cited by 38

Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and Their Homologs

Grundy, W. N., Bailey, T. L., Elkan, C., & Baker, M. E. (1997) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1997.6193 · Cited by 37

Three-dimensional structure of a complex of galanthamine (Nivalin�) with acetylcholinesterase fromTorpedo californica: Implications for the design of new anti-Alzheimer drugs

Bartolucci, C., Perola, E., Pilger, C., Fels, G., & Lamba, D. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20010201)42:2 · Cited by 151

Strategies for high‐throughput comparative modeling: Applications to leverage analysis in structural genomics and protein family organization

Mirković, N., Li, Z., Parnassa, A., & Murray, D. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21191 · Cited by 37

Impact of Template Choice on Homology Model Efficiency in Virtual Screening

Rataj, K., Witek, J., Mordalski, S., Kościółek, T., & Bojarski, A. J. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500001f · Cited by 37

Spatial clustering of protein binding sites for template based protein docking

Ghoorah, A. W., Devignes, M., Smaïl‐Tabbone, M., & Ritchie, D. W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr493 · Cited by 37

Cytotoxic species in amyloid-associated diseases: Oligomers or mature fibrils

Siddiqi, M. K., Malik, S., Majid, N., Alam, P., & Khan, R. H. (2019) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2019.06.001 · Cited by 38

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

González-Nilo, F. D., Pérez‐Acle, T., Guínez-Molinos, S., Geraldo, D. A., Sandoval, C., Yévenes, A., Santos, L. S., Laurie, V. F., Mendoza, H., & Cachau, R. E. (2011) · Biological Research · doi:10.4067/s0716-97602011000100006 · Cited by 37

In silico Protein Recombination: Enhancing Template and Sequence Alignment Selection for Comparative Protein Modelling

Contreras‐Moreira, B., Fitzjohn, P. W., & Bates, P. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00309-7 · Cited by 37

A comparison of position‐specific score matrices based on sequence and structure alignments

Panchenko, A. R., & Bryant, S. H. (2002) · Protein Science · doi:10.1110/ps.19902 · Cited by 37

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations

Schneider, J., Korshunova, K., Musiani, F., Alfonso‐Prieto, M., Giorgetti, A., & Carloni, P. (2018) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2018.01.160 · Cited by 34

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations

Alfonso‐Prieto, M., Navarini, L., & Carloni, P. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00029 · Cited by 35

Contact patterns between helices and strands of sheet define protein folding patterns

Kamat, A. P., & Lesk, A. M. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21241 · Cited by 36

The Iron−Sulfur Cluster of Electron Transfer Flavoprotein−Ubiquinone Oxidoreductase Is the Electron Acceptor for Electron Transfer Flavoprotein

Swanson, M. A., Usselman, R. J., Frerman, F. E., Eaton, G. R., & Eaton, S. S. (2008) · Biochemistry · doi:10.1021/bi800507p · Cited by 36

The valyl-tRNA synthetase from Bacillus stearothermophilus has considerable sequence homology with the isoleucyl-tRNA synthetase from Escherichia coli

Borgford, T. J., Brand, N. J., Gray, T. E., & Fersht, A. R. (1987) · Biochemistry · doi:10.1021/bi00383a012 · Cited by 36

[32] Patterson correlation searches and refinement

Brünger, A. T. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)76078-6 · Cited by 36

Molecular modeling and in vitro investigations of the human androgen receptor DNA-binding domain: application for the study of two mutations

Lobaccaro, J. A., Poujol, N., Chiche, L., Lumbroso, S., Brown, T. R., & Sultan, C. (1996) · Molecular and Cellular Endocrinology · doi:10.1016/0303-7207(95)03709-8 · Cited by 36

The SGNH hydrolase family: a template for carbohydrate diversity

Anderson, A. C., Stangherlin, S., Pimentel, K. N., Weadge, J. T., & Clarke, A. J. (2022) · Glycobiology · doi:10.1093/glycob/cwac045 · Cited by 35

Automated antibody structure prediction using Accelrys tools: Results and best practices

Fasnacht, M., Butenhof, K. J., Lamy, A., Hernandez-Guzman, F. G., Huang, H., & Yan, L. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24604 · Cited by 35

A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm

Rose, J., & Eisenmenger, F. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02102193 · Cited by 35

Structures for the Potential Drug Target Purine Nucleoside Phosphorylase from Schistosoma mansoni Causal Agent of Schistosomiasis

Pereira, H. M., Franco, G. R., Cleasby, A., & Garratt, R. C. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.08.045 · Cited by 35

Estimating quality of template‐based protein models by alignment stability

Chen, H., & Kihara, D. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21819 · Cited by 35

Macromolecular Modelling and Docking Simulations for the Discovery of Selective GPER Ligands

Rosano, C., Ponassi, M., Santolla, M. F., Pisano, A., Felli, L., Vivacqua, A., Maggiolini, M., & Lappano, R. (2015) · The AAPS Journal · doi:10.1208/s12248-015-9844-3 · Cited by 35

Protein Engineering and Stabilization from Sequence Statistics

Durani, V., & Magliery, T. J. (2013) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-394292-0.00011-4 · Cited by 35

Finding the needle in the haystack: towards solving the protein-folding problem computationally

Li, B., Fooksa, M., Heinze, S., & Meiler, J. (2017) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2017.1380596 · Cited by 39

Experimentally-driven protein structure modeling

Dokholyan, N. V. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103777 · Cited by 37

A biological cosmos of parallel universes: Does protein structural plasticity facilitate evolution?

Meier, S., & Özbek, S. (2007) · BioEssays · doi:10.1002/bies.20661 · Cited by 34

Structural and biophysical characterization of Staphylococcus aureus SaMazF shows conservation of functional dynamics

Zorzini, V., Buts, L., Sleutel, M., Garcia‐Pino, A., Talavera, A., Haesaerts, S., Greve, H. D., Cheung, A. L., van Nuland, N. A. J., & Loris, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku266 · Cited by 35

Homology model building of the HMG-1 box structural domain

Baxevanis, A. D., Bryant, S. H., & Landsman, D. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.6.1019 · Cited by 35

Expression and structural studies of fasciclin I, an insect cell adhesion molecule.

Wang, W., Zinn, K., & Björkman, P. J. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)54096-5 · Cited by 35

Systematic representation of protein folding patterns

Lesk, A. M. (1995) · Journal of Molecular Graphics · doi:10.1016/0263-7855(95)00037-7 · Cited by 35

Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold‐type I, pyridoxal‐5′‐phosphate‐dependent enzymes

Paiardini, A., Bossa, F., & Pascarella, S. (2004) · Protein Science · doi:10.1110/ps.04938104 · Cited by 35

The Salmonella YopJ-homologue AvrA does not possess YopJ-like activity

Schesser, K., Dukuzumuremyi, J., Cilio, C., Borg, S., Wallis, T. S., Pettersson, S., & Galyov, E. E. (2000) · Microbial Pathogenesis · doi:10.1006/mpat.1999.0324 · Cited by 35

Structural and functional characterization of complement c8γ, a member of the lipocalin protein family

Haefliger, J., Peitsch, M. C., Jenne, D. E., & Tschopp, J. (1991) · Molecular Immunology · doi:10.1016/0161-5890(91)90095-2 · Cited by 33

Predicting de novo the folded structure of proteins

Benner, S. A. (1992) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(92)90232-v · Cited by 35

Cel6A, a major exoglucanase from the cellulosome of the anaerobic fungi Piromyces sp. E2 and Piromyces equi

Harhangi, H. R., Freelove, A. C. J., Ubhayasekera, W., van Dinther, M., Steenbakkers, P. J. M., Akhmanova, A. S., van der DRIFT, C., Jetten, M. S. M., Mowbray, S. L., Gilbert, H. J., et al. (2003) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(03)00112-x · Cited by 34

Crystal Structure of Venezuelan Hemorrhagic Fever Virus Fusion Glycoprotein Reveals a Class 1 Postfusion Architecture with Extensive Glycosylation

Parsy, M.-L., Harlos, K., Huiskonen, J. T., & Bowden, T. A. (2013) · Journal of Virology · doi:10.1128/jvi.02298-13 · Cited by 36

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

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

Vijayabaskar, M. S., & Vishveshwara, S. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002505 · Cited by 34

Discovery of Novel Selective Serotonin Reuptake Inhibitors through Development of a Protein-Based Pharmacophore

Manepalli, S., Geffert, L. M., Surratt, C. K., & Madura, J. D. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200280m · Cited by 34

The role of molecular modelling in biomedical research

Tramontano, A. L. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.04.011 · Cited by 34

Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations

Gabrielsen, M., Ravna, A. W., Kristiansen, K., & Sylte, I. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1133-1 · Cited by 34

Crystal Structure of Mouse Carnitine Octanoyltransferase and Molecular Determinants of Substrate Selectivity*[boxs]

Jogl, G., Hsiao, Y., & Tong, L. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409894200 · Cited by 34

Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone

Reid, A. J., Yeats, C., & Orengo, C. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm355 · Cited by 34

The role of electrostatic charge in the membrane insertion of colicin A

Lakey, J. H., Parker, M. W., González‐Mañas, J. M., Duché, D., Vriend, G., Baty, D., & Pattus, F. (1994) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1994.tb18610.x · Cited by 34

Removal of the Four C-Terminal Glycine-Rich Repeats Enhances the Thermostability and Substrate Binding Affinity of Barley β-Amylase

Yue, F., Eglinton, J. K., Evans, D. E., Logue, S. J., & Langridge, P. (2000) · Biochemistry · doi:10.1021/bi000688s · Cited by 34

Comparative Protein Structure Modeling in Genomics

Sánchez, R., & Šali, A. (1999) · Journal of Computational Physics · doi:10.1006/jcph.1999.6200 · Cited by 34

Significance of structural changes in proteins: Expected errors in refined protein structures

Stroud, R. M., & Fauman, E. B. (1995) · Protein Science · doi:10.1002/pro.5560041118 · Cited by 34

Analysis of the Structural Organization and Thermal Stability of two Spermadhesins

Menéndez, M., Gasset, M., Laynez, J. L., López-Zúmel, C., Usobiaga, P., Töpfer‐Petersen, E., & Calvete, J. J. (1995) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1995.887_a.x · Cited by 34

Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions.

Briffeuil, P., Baudoux, G., Lambert, C., Bolle, X. D., Vinals, C., Feytmans, E., & Depiereux, E. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.4.357 · Cited by 34

Structure Comparison and Alignment

Bourne, P. E., & Shindyalov, I. N. (2003) · Methods of biochemical analysis · doi:10.1002/0471721204.ch16 · Cited by 34

Computational modeling of protein–RNA complex structures

Tuszyńska, I., Matelska, D., Magnus, M., Chojnowski, G., Kasprzak, J. M., Kozlowski, L. P., Dunin-Horkawicz, S., & Bujnicki, J. M. (2013) · Methods · doi:10.1016/j.ymeth.2013.09.014 · Cited by 33

MISTRAL: a tool for energy-based multiple structural alignment of proteins

Micheletti, C., & Orland, H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp506 · Cited by 33

A New Formulation of Protein Evolutionary Models that Account for Structural Constraints

Bordner, A. J., & Mittelmann, H. D. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst240 · Cited by 32

Three-dimensional structure of β-cell-specific zinc transporter, ZnT-8, predicted from the type 2 diabetes-associated gene variant SLC30A8 R325W

Weijers, R. N. M. (2010) · Diabetology & Metabolic Syndrome · doi:10.1186/1758-5996-2-33 · Cited by 33

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

Schwarzenbacher, R., Godzik, A., & Jaroszewski, L. (2007) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444907050111 · Cited by 33

A benchmark testing ground for integrating homology modeling and protein docking

Bohnuud, T., Luo, L., Wodak, S. J., Bonvin, A. M. J. J., Weng, Z., Vajda, S., Schueler‐Furman, O., & Kozakov, D. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25063 · Cited by 33

The response of protein structures to amino-acid sequence changes

Lesk, A. M., & Chothia, C. (1986) · Philosophical Transactions of the Royal Society of London Series A Mathematical and Physical Sciences · doi:10.1098/rsta.1986.0044 · Cited by 100

Comparison of conformational characteristics in structurally similar protein pairs

Flores, T. P., Orengo, C. A., Moss, D. S., & Thornton, J. M. (1993) · Protein Science · doi:10.1002/pro.5560021104 · Cited by 171

The Evolution of Protein StructuresPreprint

Chothia, C., & Lesk, A. M. (1987) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1987.052.01.046 · Cited by 88

Structural Features can be Unconserved in Proteins with Similar Folds

Russell, R. B., & Barton, G. J. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1733 · Cited by 163

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Gao, J., & Li, Z. (2009) · Biopolymers · doi:10.1002/bip.21342 · Cited by 4