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ORCIDSandor Vajda
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2020 – today
- 2024
[j35]Ayse A. Bekar-Cesaretli
, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda:
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. J. Chem. Inf. Model. 64(3): 960-973 (2024)- [j34]Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda:
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J. Chem. Inf. Model. 64(6): 2084-2100 (2024) - 2023
- [j33]Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov:
Improved prediction of MHC-peptide binding using protein language models. Frontiers Bioinform. 3 (2023) - 2022
- [j32]Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda:
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. J. Chem. Inf. Model. 62(20): 4937-4954 (2022) - 2020
- [j31]Amanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho, Dima Kozakov, György M. Keserü, Adrian Whitty, Sandor Vajda:
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J. Chem. Inf. Model. 60(12): 6612-6623 (2020)
2010 – 2019
- 2016
- [j30]Bing Xia, Sandor Vajda, Dima Kozakov:
Accounting for pairwise distance restraints in FFT-based protein-protein docking. Bioinform. 32(21): 3342-3344 (2016) - [j29]Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov:
Focused grid-based resampling for protein docking and mapping. J. Comput. Chem. 37(11): 961-970 (2016) - 2015
- [j28]Bing Xia, Artem B. Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov:
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. J. Comput. Chem. 36(20): 1568-1572 (2015) - [j27]Mohammad Moghadasi, Hanieh Mirzaei, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis, Dima Kozakov:
The Impact of Side-Chain Packing on Protein Docking Refinement. J. Chem. Inf. Model. 55(4): 872-881 (2015) - 2014
- [j26]Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda:
Docking Server for the Identification of Heparin Binding Sites on Proteins. J. Chem. Inf. Model. 54(7): 2068-2078 (2014) - [j25]Tanggis Bohnuud, Dima Kozakov, Sandor Vajda:
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces. PLoS Comput. Biol. 10(10) (2014) - [c11]Feng Nan, Mohammad Moghadasi, Pirooz Vakili, Sandor Vajda, Dima Kozakov, Ioannis Ch. Paschalidis:
A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. CDC 2014: 4623-4628 - [c10]Pirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda:
Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. CDC 2014: 5825-5830 - 2013
- [j24]Laurie E. Grove, David R. Hall, Dmitri Beglov, Sandor Vajda, Dima Kozakov:
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinform. 29(9): 1218-1219 (2013) - [c9]Mohammad Moghadasi, Dima Kozakov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis:
A new distributed algorithm for side-chain positioning in the process of protein docking. CDC 2013: 739-744 - [c8]Hanieh Mirzaei, Elizabeth A. Villar, Scott E. Mottarella, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov, Pirooz Vakili:
Flexible refinement of protein-ligand docking on manifolds. CDC 2013: 1392-1397 - 2012
- [j23]Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda:
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinform. 28(2): 286-287 (2012) - [j22]Ryan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov:
Application of asymmetric statistical potentials to antibody-protein docking. Bioinform. 28(20): 2608-2614 (2012) - [j21]David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda:
Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. J. Chem. Inf. Model. 52(1): 199-209 (2012) - [j20]Brandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov:
Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces. J. Chem. Inf. Model. 52(8): 2236-2244 (2012) - [j19]Chi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda:
FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res. 40(Web-Server-Issue): 271-275 (2012) - [c7]Mohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis:
A message passing approach to Side Chain Positioning with applications in protein docking refinement. CDC 2012: 2310-2315 - [c6]Hanieh Mirzaei, Dima Kozakov, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili:
A new approach to rigid body minimization with application to molecular docking. CDC 2012: 2983-2988
2000 – 2009
- 2009
- [j18]Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David R. Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda:
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinform. 25(5): 621-627 (2009) - [j17]Melissa R. Landon, Raquel L. Lieberman, Quyen Q. Hoang, Shulin Ju, Jose M. M. Caaveiro, Susan D. Orwig, Dima Kozakov, Ryan Brenke, Gwo-Yu Chuang, Dmitri Beglov, Sandor Vajda, Gregory A. Petsko, Dagmar Ringe:
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J. Comput. Aided Mol. Des. 23(8): 491-500 (2009) - 2008
- [j16]David W. Ritchie, Dima Kozakov, Sandor Vajda:
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinform. 24(17): 1865-1873 (2008) - [j15]Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda:
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Comput. Biol. 4(10) (2008) - [c5]Taner Kaya, Dima Kozakov, Sandor Vajda:
Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking. BIOCOMP 2008: 1028-1032 - 2007
- [j14]Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda:
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans. Autom. Control. 52(4): 664-676 (2007) - [c4]Yang Shen, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis:
Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. CDC 2007: 4545-4550 - 2006
- [c3]Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda:
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. EMBC 2006: 5330-5333 - 2005
- [j13]Shu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda:
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Res. 33(Database-Issue): 206-211 (2005) - [c2]Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, Pirooz Vakili:
A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. CDC/ECC 2005: 3675-3680 - 2004
- [j12]Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho:
ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinform. 20(1): 45-50 (2004) - [j11]Jahnavi C. Prasad, Sandor Vajda, Carlos J. Camacho:
Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res. 32(Web-Server-Issue): 50-54 (2004) - [j10]Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho:
ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. 32(Web-Server-Issue): 96-99 (2004) - 2003
- [j9]Jahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho:
Consensus alignment for reliable framework prediction in homology modeling. Bioinform. 19(13): 1682-1691 (2003) - [j8]Tamas Kortvelyesi, Michael Silberstein, Sheldon Dennis, Sandor Vajda:
Improved mapping of protein binding sites. J. Comput. Aided Mol. Des. 17(2-4): 173-186 (2003) - [c1]Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda:
Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. WABI 2003: 389-401 - 2002
- [j7]Sheldon Dennis, Sandor Vajda:
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. J. Comput. Chem. 23(3): 319-334 (2002)
1990 – 1999
- 1999
- [j6]Charles DeLisi, Sandor Vajda:
Computational problems in cell biology. Comput. Sci. Eng. 1(3): 26-32 (1999) - 1996
- [j5]Kamalakar Gulukota, Sandor Vajda, Charles DeLisi:
Peptide docking using dynamic programming. J. Comput. Chem. 17(4): 418-428 (1996) - 1994
- [j4]Ljubomir J. Buturovic, Temple F. Smith, Sandor Vajda:
Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations. J. Comput. Chem. 15(3): 300-312 (1994) - 1993
- [j3]Qiang Zheng, Rakefet Rosenfeld, Sandor Vajda, Charles DeLisi:
Loop closure via bond scaling and relaxation. J. Comput. Chem. 14(5): 556-565 (1993)
1980 – 1989
- 1987
- [j2]Sandor Vajda, P. Valkó, Keith R. Godfrey:
Direct and indirect least squares methods in continuous-time parameter estimation. Autom. 23(6): 707-718 (1987) - 1984
- [j1]P. Valkó, Sandor Vajda:
An extended ode solver for sensitivity calculations. Comput. Chem. 8(4): 255-271 (1984)
Coauthor Index
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last updated on 2024-08-05 20:21 CEST by the dblp team
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