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Recent progress and future directions in protein-protein docking
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Ritchie D.W. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9 (2008) 1-15
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CAPRI: a Critical Assessment of PRedicted Interactions
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Janin J., Henrick K., Moult J., Eyck L.T., Sternberg M.J., Vajda S., Vakser I., and Wodak S.J. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 52 (2003) 2-9
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Vajda, S.6
Vakser, I.7
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Assessment of blind predictions of protein-protein interactions: current status of docking methods
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Mendez R., Leplae R., De Maria L., and Wodak S.J. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52 (2003) 51-67
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Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
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Mendez R., Leplae R., Lensink M.F., and Wodak S.J. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60 (2005) 150-169
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36749006579
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Docking and scoring protein complexes: CAPRI 3rd Edition
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The official assessment of rounds 6-12 of CAPRI quantifies the achievements of the challenge, summarizes the methods tested and concludes that the docking field is making steady progress. The paper also gives an overview of the current state of the art in protein-protein docking.
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Lensink M.F., Méndez R., and Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 69 (2007) 704-718. The official assessment of rounds 6-12 of CAPRI quantifies the achievements of the challenge, summarizes the methods tested and concludes that the docking field is making steady progress. The paper also gives an overview of the current state of the art in protein-protein docking.
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Proteins
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Lensink, M.F.1
Méndez, R.2
Wodak SJ3
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36749098356
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The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
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Experience of the group that was the best overall performer in rounds 1-11 of the CAPRI docking experiment. The newest version of the ZDOCK program includes a pairwise potential in its scoring function, and ZRANK is a new development.
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Wiehe K., Pierce B., Tong W.W., Hwang H., Mintseris J., and Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins 69 (2007) 719-725. Experience of the group that was the best overall performer in rounds 1-11 of the CAPRI docking experiment. The newest version of the ZDOCK program includes a pairwise potential in its scoring function, and ZRANK is a new development.
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Proteins
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Wiehe, K.1
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Tong, W.W.3
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Mintseris, J.5
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Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI
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The paper describes PIPER, the first FFT-based docking program with a scoring function which includes a pairwise interaction potential, and SDU, a refinement program which takes into account the funnel-like behavior of the free energy function in a neighborhood of the native state. The group was the second best overall performer in rounds 1-11 of the CAPRI docking experiment.
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Shen Y., Brenke R., Kozakov D., Comeau S.R., Beglov D., and Vajda S. Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI. Proteins 69 (2007) 734-742. The paper describes PIPER, the first FFT-based docking program with a scoring function which includes a pairwise interaction potential, and SDU, a refinement program which takes into account the funnel-like behavior of the free energy function in a neighborhood of the native state. The group was the second best overall performer in rounds 1-11 of the CAPRI docking experiment.
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Proteins
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Shen, Y.1
Brenke, R.2
Kozakov, D.3
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Vajda, S.6
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ClusPro: performance in CAPRI rounds 6-11 and the new server
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Comeau S.R., Kozakov D., Brenke R., Shen Y., Beglov D., and Vajda S. ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins 69 (2007) 781-785
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Comeau, S.R.1
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Vajda, S.6
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Improving CAPRI predictions: optimized desolvation for rigid-body docking
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Fernández-Recio J., Abagyan R., and Totrov M. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 60 (2005) 308-313
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RosettaDock in CAPRI rounds 6-12
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This work describes the extension of RosettaDock to account for the flexibility of backbone in loop regions, and demonstrates that the method improves docking results for some of the CAPRI targets. However, the need for more extensive computations further reduces the region of the conformational space which can be explored, and hence may reduce the quality of results.
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Wang C., Schueler-Furman O., Andre I., London N., Fleishman S.J., Bradley P., Qian B., and Baker D. RosettaDock in CAPRI rounds 6-12. Proteins 69 (2007) 758-763. This work describes the extension of RosettaDock to account for the flexibility of backbone in loop regions, and demonstrates that the method improves docking results for some of the CAPRI targets. However, the need for more extensive computations further reduces the region of the conformational space which can be explored, and hence may reduce the quality of results.
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Proteins
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Wang, C.1
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Fleishman, S.J.5
Bradley, P.6
Qian, B.7
Baker, D.8
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36749077465
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Automatic prediction of protein interactions with large scale motion
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This work describes the web-based implementation of the FlexDock geometric docking algorithm which is capable of accounting for hinges in the flexible molecule. The algorithm is highly efficient and yielded the best performing server in CAPRI rounds 6-12.
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Schneidman-Duhovny D., Nussinov R., and Wolfson H.J. Automatic prediction of protein interactions with large scale motion. Proteins 69 (2007) 764-773. This work describes the web-based implementation of the FlexDock geometric docking algorithm which is capable of accounting for hinges in the flexible molecule. The algorithm is highly efficient and yielded the best performing server in CAPRI rounds 6-12.
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Proteins
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Schneidman-Duhovny, D.1
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Mashiach E., Schneidman-Duhovny D., Andrusier N., Nussinov R., and Wolfson H.J. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res 36 (2008) W229-W232
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Kowalsman N., and Eisenstein M. Inherent limitations in protein-protein docking procedures. Bioinformatics 23 (2007) 421-426
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High Ambiguity Driven biomolecular DOCKing (HADDOCK) is a relative newcomer in CAPRI, but performed extremely well when participating, in spite of using restraints based on literature data and the predictions of interface residues, rather than restraints based on experiments.
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de Vries S.J., van Dijk A.D., Krzeminski M., van Dijk M., Thureau A., Hsu V., Wassenaar T., and Bonvin A.M. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69 (2007) 726-733. High Ambiguity Driven biomolecular DOCKing (HADDOCK) is a relative newcomer in CAPRI, but performed extremely well when participating, in spite of using restraints based on literature data and the predictions of interface residues, rather than restraints based on experiments.
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Proteins
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de Vries, S.J.1
van Dijk, A.D.2
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Wassenaar, T.7
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This is the third installment of the benchmark set that became the standard in protein-protein docking and facilitates the comparison of docking methods. The 124 unbound-unbound test cases in Benchmark 3.0 are classified into 88 rigid body cases, 19 medium-difficulty cases, and 17 difficult cases, based on the degree of conformational change at the interface upon complex formation. This is 48% increase relative to Benchmark 2.0. However, some of the binary complexes are actually parts of larger multiprotein structures. Such cases may not properly test the performance of docking algorithms, and hence the benchmark set needs further analysis by the predictor groups.
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Hwang H., Pierce B., Mintseris J., Janin J., and Weng Z. Protein-protein docking benchmark version 3.0. Proteins 73 (2008) 705-709. This is the third installment of the benchmark set that became the standard in protein-protein docking and facilitates the comparison of docking methods. The 124 unbound-unbound test cases in Benchmark 3.0 are classified into 88 rigid body cases, 19 medium-difficulty cases, and 17 difficult cases, based on the degree of conformational change at the interface upon complex formation. This is 48% increase relative to Benchmark 2.0. However, some of the binary complexes are actually parts of larger multiprotein structures. Such cases may not properly test the performance of docking algorithms, and hence the benchmark set needs further analysis by the predictor groups.
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Proteins
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Vajda S. Classification of protein complexes based on docking difficulty. Proteins 60 (2005) 176-180
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Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A.A., Aflalo C., and Vakser I.A. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A 89 (1992) 2195-2199
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PIPER: an FFT-based protein docking program with pairwise potentials
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PIPER is the first fast Fourier transform (FFT)-based docking program with a scoring function which includes a structure-based interaction potential. The corresponding energy term is converted to a sum a few correlation functions using the eigenvalue-eigenvector decomposition of the matrix of interaction energy coefficients, which enables energy evaluation by the FFT correlation approach.
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Kozakov D., Brenke R., Comeau S.R., and Vajda S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 65 (2006) 392-406. PIPER is the first fast Fourier transform (FFT)-based docking program with a scoring function which includes a structure-based interaction potential. The corresponding energy term is converted to a sum a few correlation functions using the eigenvalue-eigenvector decomposition of the matrix of interaction energy coefficients, which enables energy evaluation by the FFT correlation approach.
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Proteins
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Kozakov, D.1
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Integrating statistical pair potentials into protein complex prediction
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This work describes the current version of the successful ZDOCK algorithm with a new scoring function which includes a structure-based interaction potential. It uses an optimized alphabet of 12 atom types, but is still less efficient than the eigenvalue-eigenvector decomposition used in PIPER.
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Mintseris J., Pierce B., Wiehe K., Anderson R., Chen R., and Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins 69 (2007) 511-520. This work describes the current version of the successful ZDOCK algorithm with a new scoring function which includes a structure-based interaction potential. It uses an optimized alphabet of 12 atom types, but is still less efficient than the eigenvalue-eigenvector decomposition used in PIPER.
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Proteins
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This is the main publication describing the successful RosettaDock docking method based on a Monte Carlo minimization algorithm. Owing to the detailed and fairly accurate scoring function and the repacking of interface side chains, RosettaDock can achieve remarkable accuracy, and set a new standard in protein-protein docking for cases in which the information on the binding mode helped to chose appropriate starting conformations for the complex.
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Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331 (2003) 281-299. This is the main publication describing the successful RosettaDock docking method based on a Monte Carlo minimization algorithm. Owing to the detailed and fairly accurate scoring function and the repacking of interface side chains, RosettaDock can achieve remarkable accuracy, and set a new standard in protein-protein docking for cases in which the information on the binding mode helped to chose appropriate starting conformations for the complex.
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Wang C., Bradley P., and Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 373 (2007) 503-519
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Dominguez C., Boelens R., and Bonvin A.M.J.J. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J Am Chem Soc 125 (2003) 1731-1737
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This work describes the first web-based protein-protein-docking server. Since its release in December 2004, the server has performed close to 20 000 docking calculations for more than 2000 users, resulting in over 100 publications.
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Comeau S.R., Gatchell D.W., Vajda S., and Camacho C.J. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20 (2004) 45-50. This work describes the first web-based protein-protein-docking server. Since its release in December 2004, the server has performed close to 20 000 docking calculations for more than 2000 users, resulting in over 100 publications.
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Bioinformatics
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Comeau, S.R.1
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Kozakov D., Clodfelter K.H., Vajda S., and Camacho C.J. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 89 (2005) 867-875
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Comparison of clustering algorithms for picking up near-native docking conformations generated by four FFT-based protein-protein-docking methods. It shows that the ranking based on clustering is better than that by the inherent scoring functions.
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Lorenzen S., and Zhang Y. Identification of near-native structures by clustering protein docking conformations. Proteins 68 (2007) 187-194. Comparison of clustering algorithms for picking up near-native docking conformations generated by four FFT-based protein-protein-docking methods. It shows that the ranking based on clustering is better than that by the inherent scoring functions.
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Proteins
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Large-scale docking studies show that the number of distinct energy basins is generally small and correlated with the known binding modes, which provides the conceptual basis for retaining a moderate number of the largest clusters for refinement.
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O'Toole N., and Vakser I.A. Large-scale characteristics of the energy landscape in protein-protein interactions. Proteins 71 (2008) 144-152. Large-scale docking studies show that the number of distinct energy basins is generally small and correlated with the known binding modes, which provides the conceptual basis for retaining a moderate number of the largest clusters for refinement.
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Proteins
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Paschalidis I., Shen Y., Vakili P., and Vajda S.S.D.U. A semi-definite programming-based underestimation method for global optimization in molecular docking. IEEE Trans Autom Control 52 (2007) 664-676
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Given a set of local minima, SDU constructs an underestimating function, selects new points in the conformational space close to the minimum of the underestimator as starting points for local minimization, updates the set of local minima, and iterates these steps until convergence.
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Shen Y., Paschalidis I., Vakili P., and Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol 4 (2008) e1000191. Given a set of local minima, SDU constructs an underestimating function, selects new points in the conformational space close to the minimum of the underestimator as starting points for local minimization, updates the set of local minima, and iterates these steps until convergence.
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A machine-learning algorithm was used to distinguish ensembles of low-energy conformations around the native conformation from other low-energy ensembles. The resulting classifier, FunHunt, identified the native orientation in 50/52 protein complexes in a test set, and showed that the energy decrease of trajectories toward near-native orientations is significantly larger than for other orientations.
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London N., and Schueler-Furman O. Funnel hunting in a rough terrain. learning and discriminating native energy funnels. Structure 16 (2008) 269-279. A machine-learning algorithm was used to distinguish ensembles of low-energy conformations around the native conformation from other low-energy ensembles. The resulting classifier, FunHunt, identified the native orientation in 50/52 protein complexes in a test set, and showed that the energy decrease of trajectories toward near-native orientations is significantly larger than for other orientations.
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Since structures at narrow minima lose more entropy, some of the non-native states can be detected by determining whether or not a local minimum is surrounded by a broad region of attraction on the energy surface. The analysis is based on starting Monte Carlo minimization (MCM) runs from random points around each minimum, and observing whether a certain fraction of trajectories converge to a small region within the cluster. It was shown that using global docking, dividing the conformational space into clusters and determining the stability of each cluster, the combined approach is less dependent on a priori information than exploring the potential conformational space by MCMs alone.
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Kozakov D., Schueler-Furman O., and Vajda S. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins 72 (2008) 993-1004. Since structures at narrow minima lose more entropy, some of the non-native states can be detected by determining whether or not a local minimum is surrounded by a broad region of attraction on the energy surface. The analysis is based on starting Monte Carlo minimization (MCM) runs from random points around each minimum, and observing whether a certain fraction of trajectories converge to a small region within the cluster. It was shown that using global docking, dividing the conformational space into clusters and determining the stability of each cluster, the combined approach is less dependent on a priori information than exploring the potential conformational space by MCMs alone.
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Proteins
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A combination of rescoring and refinement significantly improves protein docking performance
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This work shows that refining global docking predictions from ZDOCK using RosettaDock, and selecting the best models based on their ZRANK score substantially improves model accuracy.
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Pierce B., and Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins 72 (2008) 270-279. This work shows that refining global docking predictions from ZDOCK using RosettaDock, and selecting the best models based on their ZRANK score substantially improves model accuracy.
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Proteins
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