Molecular Docking Algorithm Based on Shape Complementarity Principles

References:

If you use this program, please cite 1 and 2:

1. Duhovny D, Nussinov R, Wolfson HJ. Efficient Unbound Docking of Rigid Molecules. In Gusfield et al., Ed. Proceedings of the 2'nd Workshop on Algorithms in Bioinformatics(WABI) Rome, Italy, Lecture Notes in Computer Science 2452, pp. 185-200, Springer Verlag, 2002 [ PDF file ]
2. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucl. Acids. Res. 33: W363-367, 2005. [ Full text ]

3. Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ. Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins. 2003 Jul 1; 52(1): 107-12. [ Abstract ] [ PDF file ]
4. Mashiach E, Schneidman-Duhovny D, Peri A, Shavit Y, Nussinov R, Wolfson HJ. An integrated suite of fast docking algorithms. Proteins. 2010 Nov 15;78(15):3197-204. [ Abstract ]

PatchDock was used in the studies below

• Protein-Protein Recognition between Acyltransferases and Acyl Carrier Proteins in Multimodular Polyketide Synthases Fong T. Wong, Alice Y. Chen, David E. Cane and Chaitan Khosla. Biochemistry 2010
• In Silico Analysis of Human Granulocyte Macrophage Colony Stimulating Factor (hGM-CSF) Gene to Increase the Stability of Gene Product. S Balaji, A Ganesh, R Maharajapuram, D Swaminathan. Journal of Computational Intelligence in Bioinformatics 2009
• A model for the interaction between NF-kappa-B and ASPP2 suggests an I-kappa-B-like binding mechanism. Hadar Benyamini, Hadas Leonov, Shahar Rotem, Chen Katz, Isaiah T. Arkin, Assaf Friedler. Proteins 2009
• Inhibition of rat hepatic CYP2E1 by quinacrine: molecular modeling investigation and effects on 4-(methyl nitrosamino)- 1-(3-pyridyl)-1-butanone (NNK)-induced mutagenicity. Petros Nikolaos Karamanakos, D.T.P. Trafalis, G.D. Geromichalos, P. Pappa, Æ P. Harkit,iM. Konstandi, M. Marselo. Arch Toxicol 2009
• In Silico identification of catalytic residues in azobenzene reductase from bacillus subtilis and its docking studies with azo dyes. K Ramanathan, V Shanthi, R Sethumadhavan. Interdisciplinary Sciences: Computational Life Sciences 2009
• Potential immunoregulatory role of heme oxygenase-1 in human milk: a combined biochemical and molecular modeling approach. Giovanni Li Volti, Fabio Galvano, Alessandro Frigiola, Salvatore Guccione, Claudia Di Giacomo, Stefano Forte, Giovanni Tringali, Massimo Caruso, Olayiwola Adedotun Adekoya and Diego Gazzolo. The Journal of Nutritional Biochemistry 2009
• Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of Their Assembly. K Lasker, M Topf, A Sali, HJ Wolfson. Journal of Molecular Biology 2009
• Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and FMN, at high resolution. Yuichi Sato, Satoshi Shimizu, Akashi Ohtaki, Keiichi Noguchi, Hideyuki Miyatake, Naoshi Dohmae, Satoshi Sasaki, Masafumi Odaka, and Masafumi Yohda. J. Bacteriol. 2009
• Prediction of localization and interactions of apoptotic proteins. Miroslav Vařech,a Michal Zimmermann, Jana Amrichová Vladimír Ulman, Pavel Matula, Michal Kozubek. J Biomed Sci. 2009
• Protein-protein docking using region-based 3D Zernike descriptors. Vishwesh Venkatraman, Yifeng D Yang, Lee Sael, Daisuke Kihara. BMC Bioinformatics 2009
• N- and C-terminal domains in human holocarboxylase synthetase participate in substrate recognition. Yousef I. Hassan, Hideaki Moriyama, Lars J. Olsen, Xin Bi and Janos Zempleni. Molecular Genetics and Metabolism 2009
• Human Sirt-1: Molecular Modeling and Structure-Function Relationships of an Unordered Protein. I Autiero, S Costantini, G Colonna. PLoS One 2009
• Molecular modeling studies of the interaction between Plasmodium falciparum HslU and HslV subunits. Subramaniam S, Mohmmed A, Gupta D. J Biomol Struct Dyn. 2009
• Structural and Interaction Analysis of Glycoprotein VI-binding Peptide Selected from a Phage Display Library. K Kato-Takagaki, Y Mizukoshi, Y Yoshizawa et al. The Journal of Biological Chemistry 2009
• Combining crystallography and molecular dynamics: The case of Schistosoma mansoni phospholipid glutathione peroxidase. Daniela Dimastrogiovanni, Massimiliano Anselmi, Adriana Erica Miele, Giovanna Boumis, Linn Petersson, Francesco Angelucci, Alfredo Di Nola, Maurizio Brunori, Andrea Bellelli. Proteins 2009
• Low Rate of Proteinuria in Children After Exposure to Low-Dose Melamine. V Wiwanitkit. Iranian Journal of Kidney Diseases 2009
• Geometric Analysis of Melamine Crystal: A Problematic Molecule Inducing Renal Failure in Melamine Intoxication. V Wiwanitkit. Renal Failure 2009
• Lithium: a potential estrogen signaling modulator JJ Valdés, OI Weeks. J Appl Biomed 2009
• An ab Initio Structural Model of a Nucleoside Permease Predicts Functionally Important Residues. Raquel Vald, Shirin Arastu-Kapu, Scott M. Landfear, Ujwal Shinde. The Journal of Biological Chemistry 2009
• Solution structure of the silkworm βGRP/GNBP3 N-terminal domain reveals the mechanism for β-1,3-glucan-specific recognition. Kiyohiro Takahasi, Masanori Ochiai, Masataka Horiuchi, Hiroyuki Kumeta, Kenji Ogura, Masaaki Ashida and Fuyuhiko Inagaki. PNAS 2009
• Solution Structures of Cytosolic RNA Sensor MDA5 and LGP2 C-terminal Domains: Identification of the RNA Recognition Loop in RIG-I-like Receptors. Kiyohiro Takahasi, Hiroyuki Kumeta, Natsuko Tsuduki, Ryo Narita, Taeko Shigemoto, Reiko Hirai, Mitsutoshi Yoneyama, Masataka Horiuchi,Kenji Ogura, Takashi Fujita, Fuyuhiko Inagaki. The Journal of Biological Chemistry 2009
• Anti-idiotypic antibodies: a new approach in prion research. Anja Colja Venturini, Maja Bresjanac, Tanja Vranac, Simon Koren, Mojca Narat, Mara Popovic, Vladka Жurin Šbec. BMC Immunology 2009
• Mechanistic Investigation of the Endo-α-N-acetylgalactosaminidas from Streptococcus pneumoniae R6. Lisa M. Willis, Ran Zhang, Anne Reid, Stephen G. Withers, Warren W. Wakarchuk. Biochemistry 2009
• Crystal structure and collagen-binding site of immune inhibitory receptor LAIR-1: unexpected implications for collagen binding by platelet receptor GPVI. T. Harma C. Brondijk, Talitha de Ruiter, Joost Ballering, Hans Wienk, Robert Jan Lebbink, Hugo van Ingen, Rolf Boelens, Richard W. Farndale, Linde Meyaard and Eric G. Huizinga. Blood 2009
• Characterization of 3-Ketosteroid 9α-Hydroxylase a Rieske Oxygenase in the Cholesterol Degradation Pathway of Mycobacterium tuberculosis. Jenna K. Capyk1 Igor D'Angelo, Natalie C. Strynadka, Lindsay D. Eltis. The Journal of Biological Chemistry 2009
• Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a Nanobody. KV Korotkov, E Pardon, J Steyaert, WGJ Hol. Structure 2009 (SymmDock)
• On the Inhibitory Affect of Some Dementia Drugs on DNA Polymerase β Activity. VN Vyjayanti, NS Chary, KS Rao. Neurochemical Research 2008
• Molecular basis of the interaction between the antiapoptotic Bcl-2 family proteins and the proapoptotic protein ASPP2. Chen Katz, Hadar Benyamini, Shahar Rotem, Mario Lebendiker, Tsafi Danieli, Anat Iosub, Hadar Refaely, Monica Dines, Vered Bronner, Tsafrir Bravman, Deborah E. Shalev, Stefan Rüdige, Assaf Friedler. PNAS 2008
• Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii. Preethi Ragunathan et al. Biochemical and Biophysical Research Communications 2008
• Platelet Endothelial Cell Adhesion Molecule 1 (PECAM-1) and Its Interactions with Glycosaminoglycans: 1. Molecular Modeling Studies. NS Gandhi, DR Coombe, RL Mancera. Biochemistry 2008
• Proposed Arrangement of Proteins Forming a Bacterial Type II Polyketide Synthase. Gaetano Castaldo, Jurica Zucko, Sibylle Heidelberger, Dušica Vujaklij4, Daslav Hranueli, John Cullum, Pakorn Wattana-Amorn, Matthew P. Crump, John Crosby and Paul F. Long. Chemistry & Biology 2008
• The Crystal Structure of the Platelet Activator Aggretin Reveals a Novel (αβ)2 Dimeric Structure. Elizabeth Hooley, Evangelos Papagrigorio, Alexei Navdaev, Amit V. Pand@, Jeannine M. Clemetson, Kenneth J. Clemetson and Jonas Emsley. Biochemistry 2008
• Comparative Studies on Inhibitors of HIV Protease: A Target for Drug Design. S Jayaraman, K Shah In Silico Biology 2008
• Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking. Zujun Shentu, Mohammad Al Hasan, Christopher Bystroff, and Mohammed J. Zaki. Proteins 2008
• Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme. Peter Kyomuhendo, Inge W. Nilsen, Bjørn Olav Brandsdal, Arne O. Sma. J Mol Model 2008
• Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants. Rituraj Purohita, R. Rajasekarana, C. Sudandiradossa, C. George Priya Dossa, K. Ramanathana and Sethumadhavan Rao. International Journal of Biological Macromolecules 2008
• Protein Surface Recognition: Structural Characterisation of Cytochrome c-Porphyrin Complexes. Peter B. Crowley, Prasad Ganji, Hasim Ibrahim. ChemBioChem 2008
• Molecular modelling studies of some 9-arylacridines to elucidate their possible roles in Topoisomerase I inhibition. S Bhowmik, A Bagchi, R Ghosh. International Journal of Integrative Biology, 2008
• Human Platelet 12-Lipoxygenase, New Findings about Its Activity, Membrane Binding and Low-resolution Structure. Ansari M. Aleem, Jerzy Jankun, John D. Dignam, Matthias Walther, Hartmut Kuhn, Dmitri I. Svergun and Ewa Skrzypczak-Jankun. JMB 2008 (SymmDock)
• Acetylcholinesterase-R increases germ cell apoptosis but enhances sperm motility. Inbal Mor, Ella H. Sklan, Erez Podoly, Marjorie Pick, Michal Kirschner, Leah Yogev, Sarit Bar-Sheshet Itach, Leticia Schreiber, Brian Geyer, Tsafrir Mor, Dan Grisaru, Hermona Soreq Journal of Cellular and Molecular Medicine 2008
• Structure-Based Protein Engineering for a-Amylase Inhibitory Activity of Plant Defensin Ku-Feng Lin, Tian-Ren Lee, Ping-Hsing Tsai, Ming-Pin Hsu, Ching-San Chen, Ping-Chiang Lyu. Proteins 2007
• Structural and Mechanistic Analysis of Protein Interactions in Module 3 of the 6-Deoxyerythronolide B Synthase. Yinyan Tang, Alice Y. Chen, Chu-Young Kim, David E. Cane and Chaitan Khosla. Chemistry & Biology 2007
• Antibody-protein interactions: benchmark datasets and prediction tools evaluation. JV Ponomarenko, PE Bourne. BMC Structural Biology, 2007
• Structure of human BRCA2-RAD51 by molecular docking study. Wiwanitkit V. Archives of Gynecology and Obstetrics, 2007
• Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation. Julsing MK, Vasilev NP, Schneidman-Duhovny D, Muntendam R, Woerdenbag HJ, Quax WJ, Wolfson HJ, Ionkova I, Kayser O. European Journal of Medicinal Chemistry, 2007
• Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit. Miled N, Yan Y, Hon W, Perisic O, Zvelebil M, Inbar Y, Schneidman-Duhovny D, Wolfson HJ, Backer JM, Williams RL. Science, 317:239-242, 2007
• The structure of a plant photosystem I supercomplex at 3.4A resolution. A Amunts, O Drory, N Nelson - Nature, 2007
• Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR. Zengjian Hu, Donnell Bowen, William M Southerland, Antonio del Sol, Yongping Pan, Ruth Nussinov, and Buyong Ma - PLoS Comput Biol. 2007
• Transient Protein Interactions between Cytochrome f and the Phytocyanin Umecyanin. K Sato, PB Crowley, C Dennison - Chembiochem, 2007
• Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction. JA Greenbaum et al.- J Mol Recognit, 2007
• Molecular determinants for the recruitment of the ubiquitin-ligase MuRF-1 onto M-line titin. M Mrosek et al. - The FASEB Journal, 2007
• Structural basis of the collagen-binding mode of discoidin domain receptor 2. Osamu Ichikawa, Masanori Osawa, Noritaka Nishida, Naoki Goshima, Nobuo Nomura and Ichio Shimada - The EMBO Journal, 2007
• Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data. Gihan Dawelbait, Christof Winter, Yanju Zhang, Christian Pilarsky, Robert Grutzmann, Jorg-Christian Heinrich and Michael Schroeder - Bioinformatics 2007
• Peripheral Site Acetylcholinesterase Blockade Induces RACK1-Associated Neuronal Remodeling N Farchi, K Ofek, E Podoly, H Dong, YY Xiang,S Diamant, O Livnah, J Li, B Hochner, W Lu, H Soreq - Neurodegenerative Dis. 2007
• Molecular Modeling of the Complex between the XWNT8 Protein and the CRD Domain of the MFZD8 Receptor. A. E. Voronkov, I. I. Baskin, V. A. Palyulin, and Academician N. S. Zefirov - Doklady Biochemistry and Biophysics, Springer 2007
• Modulation of Human CYP19A1 Activity by Mutant NADPH P450 Oxidoreductase A Pandey, P Kempna, G Hofer, PE Mullis, CE Fluck - Molecular Endocrinology 2007
• An Allosteric Rheostat in HIV-1 gp120 Reduces CCR5 Stoichiometry Required for Membrane Fusion and Overcomes Diverse Entry Limitations Emily J. Platt, James P. Durnin, Ujwal Shinde and David Kabat JMB 2007 (SymmDock)
• Conformational changes in the AAA ATPase p97-p47 adaptor complex F Beuron et al. - The EMBO Journal, 2006 (SymmDock)
• Formation of a Soluble Stable Complex between Pristine C60-Fullerene and a Native Blood Protein. Bogdan Belgorodsky, Ludmila Fadeev, Jenny Kolsenik, Michael Gozin - Chembiochem, 2006
• Structural Modeling of Protein Interactions by Analogy: Application to PSD-95. Dmitry Korkin, Fred P. Davis, Frank Alber, Tinh Luong, Min-Yi Shen, Vladan Lucic, Mary B. Kennedy, Andrej Sali PLoS Computational Biology, 2006
• Molecular Structure of Human Transferrin-Transferrin Receptor Complex. V Wiwanitkit - Int. J. Mol. Sci, 2006
• Modeling of the potential coiled-coil structure of snapin protein and its interaction with SNARE complex. Ragul Gowthaman, A Johnwin Silvester, K Saranya, KS Rathna Kanya, and NR Archana. Bioinformation. 2006; 1(7): 269-275.
• Structural basis for platelet collagen responses by the immune-type receptor glycoprotein V.I K Horii, ML Kahn, AB Herr - Blood, 2006
• Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids. Yaw-Jen Liu, Chao-Sheng Cheng, Szu-Ming Lai, Ming-Pin Hsu, Ching-San Chen, Ping-Chiang Lyu. Proteins 63(4): 777-786, 2006
• Structural identification of a novel thioredoxin SoxS: Prediction of the function in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. Angshuman Bagchi, and Tapash Chandra Ghosh - Journal of Molecular Structure: THEOCHEM, 2006
• Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. Angshuman Bagchi, and Tapash Chandra Ghosh - Biophysical Chemistry 2006
• Mutations in the Tight-Junction Gene Claudin 19 (CLDN19) Are Associated with Renal Magnesium Wasting, Renal Failure, and Severe Ocular Involvement. Martin Konrad et al. Am. J. Hum. Genet., 79:949-957, 2006
• High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase JL Jenkins, JJ Tanner - Acta Cryst.D, 2006
• Flavonoids Attenuate Cardiovascular Disease, Inhibit Phosphodiesterase, and Modulate Lipid Homeostasis in Adipose Tissue and Liver. Michael R. Peluso - Experimental Biology and Medicine 231:1287-1299, 2006
• Interaction of c(60)-fullerene and carboxyfullerene with proteins: docking and binding site alignment. Benyamini H, Shulman-Peleg A, Wolfson HJ, Belgorodsky B, Fadeev L, Gozin M. - Bioconjug Chem. 2006
• Model of gonadotropin-releasing hormone and gonadotropin-releasing hormone complex . V Wiwanitkit - Sexuality and Disability, 2006
• Why is there no dengue endocarditis? V Wiwanitkit - International Journal of Cardiology, 2006
• Letter to the Editor: Immune Complex: Does It Have a Role in Pathogenesis of Renal Failure in Dengue? V Wiwanitkit - Renal Failure, 2005
• Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for Docking Inbal Halperin, Haim Wolfson and Ruth Nussinov - Structure, 2004
• Identification of the N-terminal peptide binding site of glucose-regulated protein 94. Gidalevitz T, Biswas C, Ding H, Schneidman-Duhovny D, Wolfson HJ, Stevens F, Radford S, Argon Y J Biol Chem. 279:16543-52, 2004