Protein Function Prediction Using Local 3D Templates

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

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works

The Protein Data Bank

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

UniProt: the Universal Protein knowledgebase

Apweiler, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,535 · see citing works

Atlas of protein sequence and structure

Chang, M.-Y., Dayhoff, M. O., Eck, R. V., & Sochard, M. R. (1965) · NASA Technical Reports Server (NASA) · Cited by 4,383 · see citing works

Satisfying Hydrogen Bonding Potential in Proteins

McDonald, I. K., & Thornton, J. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1334 · Cited by 2,136 · see citing works

PISCES: a protein sequence culling server

Wang, G., & Dunbrack, R. L. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg224 · Cited by 1,664 · see citing works

Dali: a network tool for protein structure comparison

Holm, L., & Sander, C. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89105-7 · Cited by 1,462 · see citing works

Surprising similarities in structure comparison

Gibrat, J.-F., Madej, T., & Bryant, S. H. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80058-3 · Cited by 1,041 · see citing works

Protein superfamilles and domain superfolds

Orengo, C. A., Jones, D. T., & Thornton, J. M. (1994) · Nature · doi:10.1038/372631a0 · Cited by 786 · see citing works

ProFunc: a server for predicting protein function from 3D structure

Laskowski, R. A., Watson, J. D., & Thornton, J. M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki414 · Cited by 653 · see citing works

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.

Nagano, N., Orengo, C., & Thornton, J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00649-6 · Cited by 631 · see citing works

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

Porter, C. T. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh028 · Cited by 605 · see citing works

The relationship between protein structure and function: a comprehensive survey with application to the yeast genome

Hegyi, H., & Gerstein, M. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2661 · Cited by 421 · see citing works

Crystal structure of a bacterial chitinase at 2.3 Å resolution

Anastassis Perrakis, A., Tews, I., Dauter, Z., Oppenheim, A. B., Chet, I., Wilson, K. S., & Vorgias, C. E. (1994) · Structure · doi:10.1016/s0969-2126(94)00119-7 · Cited by 392 · see citing works

Empirical statistical estimates for sequence similarity searches

Pearson, W. R. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1525 · Cited by 335 · see citing works

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

Wallace, A. C., Borkakoti, N., & Thornton, J. M. (1997) · Protein Science · doi:10.1002/pro.5560061104 · Cited by 330 · see citing works

Predicting protein function from sequence and structural data

Watson, J. D., Laskowski, R. A., & Thornton, J. M. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.04.003 · Cited by 317 · see citing works

Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton

Kleywegt, G. J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2393 · Cited by 309 · see citing works

Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-Å resolution

van Aalten, D. M. F., Synstad, B., Brurberg, M. B., Hough, E., Riise, B. W., Eijsink, V. G. H., & Wierenga, R. K. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.11.5842 · Cited by 265 · see citing works

Derivation of 3D coordinate templates for searching structural databases: Application to ser‐His‐Asp catalytic triads in the serine proteinases and lipases

Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1996) · Protein Science · doi:10.1002/pro.5560050603 · Cited by 257 · see citing works

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Pearl, F. M. G. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki024 · Cited by 254 · see citing works

Protein folds and functions

Martin, A. C. R., Orengo, C. A., Hutchinson, E. G., Jones, S., Karmirantzou, M., Laskowski, R. A., Mitchell, J. B. O., Taroni, C., & Thornton, J. M. (1998) · Structure · doi:10.1016/s0969-2126(98)00089-6 · Cited by 217 · see citing works

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis

Barker, J., & Thornton, J. M. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg226 · Cited by 200 · see citing works

Assigning genomic sequences to CATH

Pearl, F. M. G. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.277 · Cited by 191 · see citing works

Inference of Protein Function from Protein Structure

Pal, D., & Eisenberg, D. S. (2005) · Structure · doi:10.1016/j.str.2004.10.015 · Cited by 188 · see citing works

Conservation helps to identify biologically relevant crystal contacts

Valdar, W. S. J., & Thornton, J. M. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5034 · Cited by 162 · see citing works

Overview of structural genomics: from structure to function

Zhang, C., & Kim, S.-H. (2003) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(02)00015-7 · Cited by 154 · see citing works

Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.

Anantharaman, V., Aravind, L., & Koonin, E. (2003) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(02)00018-2 · Cited by 150 · see citing works

Searching for functional sites in protein structures

Jones, S. R., & Thornton, J. M. (2003) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2003.11.001 · Cited by 147 · see citing works

Integrating Structure, Bioinformatics, and Enzymology to Discover Function

Sanishvili, R., Yakunin, A. F., Laskowski, R. A., Skarina, T., Evdokimova, E., Doherty-Kirby, A. L., Lajoie, G., Thornton, J. M., Arrowsmith, C. H., Savchenko, A. V., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303867200 · Cited by 126 · see citing works

Barrel structures in proteins: Automatic identification and classification including a sequence analysis of TIM barrels

Nagano, N., Hutchinson, E. G., & Thornton, J. M. (1999) · Protein Science · doi:10.1110/ps.8.10.2072 · Cited by 72 · see citing works

An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence

Yang, A., & Honig, B. H. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3974 · Cited by 65 · see citing works

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 · see citing works

RECOGNIZING COMPLEX, ASYMMETRIC FUNCTIONAL SITES IN PROTEIN STRUCTURES USING A BAYESIAN SCORING FUNCTION

Wei, L., & Altman, R. B. (2003) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720003000150 · Cited by 32 · see citing works

Efficient identification of side‐chain patterns using a multidimensional index tree

Hamelryck, T. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10338 · Cited by 29 · see citing works

The Impact of Structural Genomics on the Protein Data Bank

Berman, H. M., & Westbrook, J. (2004) · American Journal of PharmacoGenomics · doi:10.2165/00129785-200404040-00004 · Cited by 28 · see citing works

Structural Proteomics: Inferring Function from Protein Structure

Wild, D. L., & Saqi, M. A. S. (2004) · Current Proteomics · doi:10.2174/1570164043488234 · Cited by 17 · see citing works

Crystal structure of an α/β serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 Å resolution

Arndt, J. W., Schwarzenbacher, R., Page, R., Abdubek, P., Ambing, E., Biorac, T., Cánaves, J. M., Chiu, H., Dai, X., Deacon, A. M., et al. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20336 · Cited by 15 · see citing works

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2340 · Cited by 1,028 · see citing works

A structural biology community assessment of AlphaFold2 applications

Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00849-w · Cited by 675 · see citing works

Predicting protein function from sequence and structure

Lee, D., Redfern, O., & Orengo, C. A. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2281 · Cited by 572 · see citing works

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

Johansson, M. U., Zoete, V., Michielin, O. A., & Guex, N. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-173 · Cited by 404 · see citing works

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

Xie, L., Li, J., Xie, L., & Bourne, P. E. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000387 · Cited by 249 · see citing works

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments

Xie, L., & Bourne, P. E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704422105 · Cited by 245 · see citing works

Three-dimensional protein structure prediction: Methods and computational strategies

Dorn, M., Silva, M. B. E., Buriol, L. S., & Lamb, L. C. (2014) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2014.10.001 · Cited by 210 · see citing works

ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

Cao, R., Freitas, C., Chan, L., Sun, M., Jiang, H., & Chen, Z. (2017) · Molecules · doi:10.3390/molecules22101732 · Cited by 203 · see citing works

Advances in Protein Chemistry and Structural Biology

(2021) · Advances in protein chemistry and structural biology · doi:10.1016/s1876-1623(21)00003-1 · Cited by 174 · see citing works

Information theory applied to the sparse gene ontology annotation network to predict novel gene function

Tao, Y., Sam, L. T., Li, J., Friedman, C., & Lussier, Y. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm195 · Cited by 159 · see citing works

Structure-based systems biology for analyzing off-target binding

Xie, L., Xie, L., & Bourne, P. E. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.004 · Cited by 152 · see citing works

A structural biology community assessment of AlphaFold 2 applications

Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · doi:10.1101/2021.09.26.461876 · Cited by 122 · see citing works

Exploring the structure and function paradigm.

Redfern, O., Dessailly, B. H., & Orengo, C. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.05.007 · Cited by 133 · see citing works

AlphaFold2 protein structure prediction: Implications for drug discovery

Borkakoti, N., & Thornton, J. M. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102526 · Cited by 137 · see citing works

Structural Relationships in the Lysozyme Superfamily: Significant Evidence for Glycoside Hydrolase Signature Motifs

Wohlkönig, A., Huet, J., Looze, Y., & Wintjens, R. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015388 · Cited by 121 · see citing works

FUNCTION PREDICTION OF UNCHARACTERIZED PROTEINS

Hawkins, T., & Kihara, D. (2007) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720007002503 · Cited by 109 · see citing works

A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate

Lauck, M., Sibley, S. D., Lara, J., Purdy, M. A., Khudyakov, Y. E., Hyeroba, D., Tumukunde, A., Weny, G., Switzer, W. M., Chapman, C. A., et al. (2013) · Journal of Virology · doi:10.1128/jvi.00888-13 · Cited by 98 · see citing works

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

Xie, L., Xie, L., & Bourne, P. E. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp220 · Cited by 93 · see citing works

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

Pires, D. E. V., de Melo-Minardi, R. C., dos Santos, M. A., da Silveira, C. H., Santoro, M. M., & Meira, W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-s4-s12 · Cited by 92 · see citing works

Comparison of protein active site structures for functional annotation of proteins and drug design

Powers, R., Copeland, J. C., Germer, K., Mercier, K., Ramanathan, V., & Revesz, P. Z. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21092 · Cited by 91 · see citing works

Robust recognition of zinc binding sites in proteins

Ebert, J. C., & Altman, R. B. (2007) · Protein Science · doi:10.1110/ps.073138508 · Cited by 90 · see citing works

Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks

Cao, R., & Cheng, J. J. (2015) · Methods · doi:10.1016/j.ymeth.2015.09.011 · Cited by 89 · see citing works

Structure-based function prediction: approaches and applications

Gherardini, P. F., & Helmer‐Citterich, M. (2008) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/eln030 · Cited by 87 · see citing works

Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study

Watson, J. D., Sanderson, S., Ezersky, A., Savchenko, A. V., Edwards, A. M., Orengo, C. A., Joachimiak, A., Laskowski, R. A., & Thornton, J. M. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.063 · Cited by 79 · see citing works

Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features

Nimrod, G., Szilágyi, A., Leslie, C. S., & Ben‐Tal, N. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.02.023 · Cited by 78 · see citing works

HotPatch: A Statistical A pproach to Finding Biologically Relevant Features on Protein Surfaces

Pettit, F. K., Bare, E., Tsai, A. G., & Bowie, J. U. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.03.036 · Cited by 76 · see citing works

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Kristensen, D. M., Ward, R. M., Lisewski, A. M., Erdin, S., Chen, B. Y., Fofanov, V. Y., Kimmel, M., Kavraki, L. E., & Lichtarge, O. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-17 · Cited by 74 · see citing works

Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites

Binkowski, T. A., & Joachimiak, A. (2008) · BMC Structural Biology · doi:10.1186/1472-6807-8-45 · Cited by 72 · see citing works

Detection of Functionally Important Regions in “Hypothetical Proteins” of Known Structure

Nimrod, G., Schushan, M., Steinberg, D. M., & Ben‐Tal, N. (2008) · Structure · doi:10.1016/j.str.2008.10.017 · Cited by 70 · see citing works

Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns

Tseng, Y. Y., Dundas, J., & Liang, J. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.072 · Cited by 62 · see citing works

Verification of a topology model of PorT as an integral outer-membrane protein in Porphyromonas gingivalis

Nguyen, K.-A. T., Żylicz, J., Szczęsny, P., Sroka, A., Hunter, N., & Potempa, J. (2009) · Microbiology · doi:10.1099/mic.0.024323-0 · Cited by 62 · see citing works

Graphlet Kernels for Prediction of Functional Residues in Protein Structures

Vacic, V., Iakoucheva, L. M., Lonardi, S., & Predrag Radivojac, A. (2010) · Journal of Computational Biology · doi:10.1089/cmb.2009.0029 · Cited by 55 · see citing works

Prediction of Functional Sites Based on the Fuzzy Oil Drop Model

Bryliński, M., Wiklik, K., Jurkowski, W., Kochańczyk, M., Stawowczyk, E., Konieczny, L., & Roterman, I. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030094 · Cited by 55 · see citing works

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

Chartier, M., Gaudreault, F., & Najmanovich, R. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts149 · Cited by 51 · see citing works

Functional and Structural Analysis of the Siderophore Synthetase AsbB through Reconstitution of the Petrobactin Biosynthetic Pathway from Bacillus anthracis

Nusca, T. D., Kim, Y., Maltseva, N., Lee, J. Y., Eschenfeldt, W. H., Stols, L. M., Schofield, M. M., Scaglione, J. B., Dixon, S. D., Oves‐Costales, D., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.359349 · Cited by 50 · see citing works

Enzyme function and evolution through the lens of bioinformatics

Ribeiro, A. J. M., Riziotis, I. G., Borkakoti, N., & Thornton, J. M. (2023) · Biochemical Journal · doi:10.1042/bcj20220405 · Cited by 50 · see citing works

FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies

Redfern, O., Dessailly, B. H., Dallman, T. J., Sillitoe, I., & Orengo, C. A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000485 · Cited by 49 · see citing works

Template-based prediction of protein function

Petrey, D. S., Chen, T. S., Deng, L., Garzón, J. I., Hwang, H., Lasso, G., Lee, H., Silkov, A., & Honig, B. H. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.01.007 · Cited by 47 · see citing works

The Structure of a Conserved Piezo Channel Domain Reveals a Topologically Distinct β Sandwich Fold

Kamajaya, A., Kaiser, J. T., Lee, J., Reid, M., & Rees, D. C. (2014) · Structure · doi:10.1016/j.str.2014.08.009 · Cited by 46 · see citing works

Protein function prediction: towards integration of similarity metrics

Erdin, S., Lisewski, A. M., & Lichtarge, O. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.02.001 · Cited by 46 · see citing works

A review of machine learning-based methods for predicting drug–target interactions

Shi, W., Yang, H. T., Xie, L., Yin, X.-X., & Zhang, Y. (2024) · Health Information Science and Systems · doi:10.1007/s13755-024-00287-6 · Cited by 46 · see citing works

Prediction and experimental validation of enzyme substrate specificity in protein structures

Amin, S. R., Erdin, S., Ward, R. M., Lua, R. C., & Lichtarge, O. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305162110 · Cited by 45 · see citing works

Exploring the other side of biologically relevant chemical space: Insights into carboxylic, sulfonic and phosphonic acid bioisosteric relationships

Macchiarulo, A., & Pellicciari, R. (2007) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2007.04.010 · Cited by 45 · see citing works

Structure‐based function inference using protein family‐specific fingerprints

Bandyopadhyay, D., Huan, J., Liu, J., Prins, J. F., Snoeyink, J. S., Wang, W., & Tropsha, A. (2006) · Protein Science · doi:10.1110/ps.062189906 · Cited by 45 · see citing works

Evolutionary Trace Annotation of Protein Function in the Structural Proteome

Erdin, S., Ward, R. M., Venner, E., & Lichtarge, O. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.12.037 · Cited by 44 · see citing works

Bridging protein local structures and protein functions

Liu, Z., Wu, L., Wang, Y., Zhang, X., & Chen, L. (2008) · Amino Acids · doi:10.1007/s00726-008-0088-8 · Cited by 43 · see citing works

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs

Chen, B. Y., Fofanov, V. Y., Bryant, D., Dodson, B. D., Kristensen, D. M., Lisewski, A. M., Kimmel, M., Lichtarge, O., & Kavraki, L. E. (2007) · Journal of Computational Biology · doi:10.1089/cmb.2007.r017 · Cited by 41 · see citing works

CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction

Wu, Z., Guo, M., Jin, X., Chen, J., & Liu, B. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad123 · Cited by 39 · see citing works

Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction

Prymula, K., Jadczyk, T., & Roterman, I. (2010) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-010-9402-0 · Cited by 38 · see citing works

LSTrAP: efficiently combining RNA sequencing data into co-expression networks

Proost, S., Krawczyk, A., & Mutwil, M. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1861-z · Cited by 38 · see citing works

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Banerjee, S., Bhandary, P., Woodhouse, M. R., Sen, T. Z., Wise, R. P., & Andorf, C. M. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04120-9 · Cited by 38 · see citing works

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles

Xie, Z., & Hwang, M. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts182 · Cited by 36 · see citing works

QM/MM methodology, docking and spectroscopic (FT-IR/FT-Raman, NMR, UV) and Fukui function analysis on adrenergic agonist

Maheswari, J. U., Muthu, S., & Sundius, T. (2014) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2014.07.095 · Cited by 34 · see citing works

LIBRA-WA: a web application for ligand binding site detection and protein function recognition

Toti, D., Hung, L. V., Tortosa, V., Brandi, V., & Polticelli, F. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx715 · Cited by 33 · see citing works

Computational analyses of the surface properties of protein–protein interfaces

Gruber, J., Zawaira, A., Saunders, R., Barrett, C. P., & Noble, M. E. M. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906046762 · Cited by 33 · see citing works

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

Kristensen, D. M., Chen, B. Y., Fofanov, V. Y., Ward, R. M., Lisewski, A. M., Kimmel, M., Kavraki, L. E., & Lichtarge, O. (2006) · Protein Science · doi:10.1110/ps.062152706 · Cited by 33 · see citing works

GASS: identifying enzyme active sites with genetic algorithms

Izidoro, S. C., de Melo-Minardi, R. C., & Pappa, G. L. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu746 · Cited by 32 · see citing works

Comparison of structure‐based and threading‐based approaches to protein functional annotation

Bryliński, M., & Skolnick, J. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22566 · Cited by 31 · see citing works

Evolution: a guide to perturb protein function and networks

Lichtarge, O., & Wilkins, A. D. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.04.002 · Cited by 29 · see citing works

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

Lee, D., Das, S., Dawson, N. L., Dobrijevic, D., Ward, J. M., & Orengo, C. A. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004926 · Cited by 30 · see citing works

Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin

Arenas, N. E., Salazar, L. M., Soto, C. Y., Vizcaíno, C., Patarroyo, M. E., Patarroyo, M. A., & Gómez, A. (2011) · BMC Structural Biology · doi:10.1186/1472-6807-11-16 · Cited by 30 · see citing works

Discovery of Similar Regions on Protein Surfaces

Bock, M. E., Garutti, C., & Guerra, C. (2007) · Journal of Computational Biology · doi:10.1089/cmb.2006.0145 · Cited by 27 · see citing works

Computational Methods for Identification of Functional Residues in Protein Structures

Xin, F., & Predrag Radivojac, A. (2011) · Current Protein and Peptide Science · doi:10.2174/138920311796957685 · Cited by 26 · see citing works

LIBRA: LIgand Binding site Recognition Application

Hung, L. V., Caprari, S., Bizai, M., Toti, D., & Polticelli, F. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv489 · Cited by 26 · see citing works

The ProFunc Function Prediction Server

Laskowski, R. A. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7015-5_7 · Cited by 26 · see citing works

BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server

Xiong, B., Wu, J., Burk, D. L., Xue, M., Jiang, H., & Shen, J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-47 · Cited by 25 · see citing works

Metric learning for enzyme active-site search

Kato, T., & Nagano, N. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq519 · Cited by 24 · see citing works

QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs

Smaili, F. Z., Tian, S., Roy, A., Alazmi, M., Arold, S. T., Mukherjee, S., Hefty, P. S., Chen, W., & Gao, X. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.02.001 · Cited by 23 · see citing works

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation

Wallach, I., & Lilien, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp204 · Cited by 23 · see citing works

De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features

Ward, R. M., Erdin, S., Tran, T. A., Kristensen, D. M., Lisewski, A. M., & Lichtarge, O. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002136 · Cited by 22 · see citing works

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction

Chen, B. Y., Fofanov, V. Y., Bryant, D., Dodson, B. D., Kristensen, D. M., Lisewski, A. M., Kimmel, M., Lichtarge, O., & Kavraki, L. E. (2006) · Lecture notes in computer science · doi:10.1007/11732990_42 · Cited by 22 · see citing works

Identification of protein functional surfaces by the concept of a split pocket

Tseng, Y. Y., & Li, W. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22402 · Cited by 22 · see citing works

The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation

Wu, S., Liang, M., & Altman, R. B. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r8 · Cited by 22 · see citing works

The Crystal Structure of a Human PP2A Phosphatase Activator Reveals a Novel Fold and Highly Conserved Cleft Implicated in Protein-Protein Interactions

Magnúsdóttir, A., Stenmark, P., Flodin, S., Nyman, T., Hammarström, M., Ehn, M., H., M. A. B., Berglund, H., & Nordlund, P. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.c600100200 · Cited by 22 · see citing works

Understanding the cell in terms of structure and function: insights from structural genomics

Rigden, D. J. (2006) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2006.07.004 · Cited by 21 · see citing works

The Poisson Index: a new probabilistic model for protein–ligand binding site similarity

Davies, J. R., Jackson, R. M., Mardia, K. V., & Taylor, C. C. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm470 · Cited by 21 · see citing works

Function Prediction of Rv0079, A HypotheticalMycobacterium tuberculosisDosR Regulon Protein

Mishra, S. (2009) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2009.10507316 · Cited by 21 · see citing works

Understand protein functions by comparing the similarity of local structural environments

Chen, J., Xie, Z., & Wu, Y. (2016) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2016.11.008 · Cited by 19 · see citing works

A three-way approach for protein function classification

Rehman, H. U., Azam, N., Yao, J., & Benso, A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0171702 · Cited by 19 · see citing works

Accurate Protein Structure Annotation through Competitive Diffusion of Enzymatic Functions over a Network of Local Evolutionary Similarities

Venner, E., Lisewski, A. M., Erdin, S., Ward, R. M., Amin, S. R., & Lichtarge, O. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014286 · Cited by 19 · see citing works

CAVITY-AWARE MOTIFS REDUCE FALSE POSITIVES IN PROTEIN FUNCTION PREDICTION

Chen, B. Y., Bryant, D., Fofanov, V. Y., Kristensen, D. M., Cruess, A. E., Kimmel, M., Lichtarge, O., & Kavraki, L. E. (2006) · IEEE Computational Systems Bioinformatics Conference (CSB) · doi:10.1142/9781860947575_0037 · Cited by 19 · see citing works

Capturing the geometry, function, and evolution of enzymes with 3D templates

Riziotis, I. G., & Thornton, J. M. (2022) · Protein Science · doi:10.1002/pro.4363 · Cited by 18 · see citing works

A protein sequence meta-functional signature for calcium binding residue prediction

Horst, J. A., & Samudrala, R. (2010) · Pattern Recognition Letters · doi:10.1016/j.patrec.2010.04.012 · Cited by 18 · see citing works

Sequence and Structural Features of Enzymes and their Active Sites by EC Class

Bray, T., Doig, A. J., & Warwicker, J. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.11.057 · Cited by 18 · see citing works

Integrating biological data through the genome

Reeves, G. A., & Thornton, J. M. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl086 · Cited by 18 · see citing works

Functional annotation strategy for protein structures

Doppelt‐Azeroual, O., Moriaud, F., Bornot, A., & de Brevern, A. G. (2007) · Bioinformation · doi:10.6026/97320630001357 · Cited by 17 · see citing works

Sub-AQUA: real-value quality assessment of protein structure models

Yang, Y. D., Spratt, P., Chen, H., Park, C., & Kihara, D. (2010) · Protein Engineering Design and Selection · doi:10.1093/protein/gzq030 · Cited by 17 · see citing works

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction

Bryant, D., Moll, M., Chen, B. Y., Fofanov, V. Y., & Kavraki, L. E. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-242 · Cited by 16 · see citing works

The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities

(2023) · doi:10.1016/j.jmb.2023.168254 · Cited by 15 · see citing works

On the Relationship Between Catalytic Residues and their Protein Contact Number

Huang, S., Yu, S., Shih, C., Guan, H.-W., Huang, T.-T., & Hwang, J. (2011) · Current Protein and Peptide Science · doi:10.2174/138920311796957676 · Cited by 15 · see citing works

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

Kurbatova, N., Chartier, M., Zylber, M. I., & Najmanovich, R. (2013) · F1000Research · doi:10.12688/f1000research.2-117.v1 · Cited by 15 · see citing works

Ligands in PSI structures

Kumar, A., Chiu, H., Axelrod, H. L., Morse, A. T., Elsliger, M., Wilson, I. A., & Deacon, A. M. (2010) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309110008092 · Cited by 15 · see citing works

1,000 structures and more from the MCSG

Lee, D., de Beer, T., Laskowski, R. A., Thornton, J. M., & Orengo, C. A. (2011) · BMC Structural Biology · doi:10.1186/1472-6807-11-2 · Cited by 15 · see citing works

MATCHING OF STRUCTURAL MOTIFS USING HASHING ON RESIDUE LABELS AND GEOMETRIC FILTERING FOR PROTEIN FUNCTION PREDICTION

Moll, M., & Kavraki, L. E. (2008) · IEEE Computational Systems Bioinformatics Conference (CSB) · doi:10.1142/9781848162648_0014 · Cited by 15 · see citing works

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development

Bandyopadhyay, D., Huan, J., Prins, J. F., Snoeyink, J. S., Wang, W., & Tropsha, A. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9273-4 · Cited by 15 · see citing works

Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues

Wu, S., Liu, T., & Altman, R. B. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-4 · Cited by 15 · see citing works

Loxoscelism: Advances and Challenges in the Design of Antibody Fragments with Therapeutic Potential

Karim-Silva, S., Becker-Finco, A., Jiacomini, I. G., Boursin, F., Leroy, A., Noiray, M., de Moura, J. F., Aubrey, N., Billiald, P., & Alvarenga, L. M. (2020) · Toxins · doi:10.3390/toxins12040256 · Cited by 14 · see citing works

Identification of two novel HSP90 proteins in Babesia orientalis: molecular characterization, and computational analyses of their structure, function, antigenicity and inhibitor interaction

Khan, M. K., He, L., Zhang, W., Wang, Y., Tao, Q., Song, Q., Sajid, M. S., Yu, Q., Hu, J., Fang, R., et al. (2014) · Parasites & Vectors · doi:10.1186/1756-3305-7-293 · Cited by 14 · see citing works

Crystal Structure of the Three Tandem FF Domains of the Transcription Elongation Regulator CA150

Lu, M., Yang, J., Ren, Z. J., Sabui, S. K., Espejo, A. B., Bedford, M. T., Jacobson, R. H., Jeruzalmi, D., McMurray, J. S., & Chen, X. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.086 · Cited by 14 · see citing works

Predicting Protein Functions from Protein Interaction Networks

Chua, H. N., & Wong, L. (2012) · International Journal of Knowledge Discovery in Bioinformatics · doi:10.4018/ijkdb.2012100104 · Cited by 14 · see citing works

Capturing the geometry, function, and evolution of enzymes with 3D templates

Riziotis, I. G., & Thornton, J. M. (2022) · Protein Science · doi:10.1002/pro.4363 · Cited by 18 · see citing works

Template-based prediction of protein function

Petrey, D. S., Chen, T. S., Deng, L., Garzón, J. I., Hwang, H., Lasso, G., Lee, H., Silkov, A., & Honig, B. H. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.01.007 · Cited by 47 · see citing works

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Kristensen, D. M., Ward, R. M., Lisewski, A. M., Erdin, S., Chen, B. Y., Fofanov, V. Y., Kimmel, M., Kavraki, L. E., & Lichtarge, O. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-17 · Cited by 74 · see citing works

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

Wallace, A. C., Borkakoti, N., & Thornton, J. M. (1997) · Protein Science · doi:10.1002/pro.5560061104 · Cited by 330 · see citing works

Case Studies: Function Predictions of Structural Genomics Results

Watson, J. D., Laskowski, R. A., & Thornton, J. M. (2017) · Springer eBooks · doi:10.1007/978-94-024-1069-3_14 · Cited by 1 · see citing works