Ultrahigh-Throughput Virtual Screening Strategies against PPI Targets: A Case Study of STAT Inhibitors.

György M. Keserü https://orcid.org/0000-0003-1039-7809

Tibor Viktor Szalai Nikolett Péczka Levente Sipos-Szabó László Petri Dávid Bajusz György M. Keserü Ultrahigh-Throughput Virtual Screening Strategies against PPI Targets: A Case Study of STAT Inhibitors. 7734-7748 2025 65 J. Chem. Inf. Model. 14 https://doi.org/10.1021/acs.jcim.5c00907 db/journals/jcisd/jcisd65.html#SzalaiPSPBK25 streams/journals/jcisd

Sonja Peter Lydia Siragusa Morgan C. Thomas Tommaso Palomba Simon Cross Noel M. O'Boyle Dávid Bajusz György G. Ferenczy György M. Keserü Giovanni Bottegoni Brian Joseph Bender I-Jen Chen Chris de Graaf Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential. 8176-8192 2024 64 J. Chem. Inf. Model. 21 https://doi.org/10.1021/acs.jcim.4c00819 db/journals/jcisd/jcisd64.html#PeterSTPCOBFKBBCG24 streams/journals/jcisd

Levente M. Mihalovits Tibor Viktor Szalai Dávid Bajusz György M. Keserü Exploring Chemical Spaces in the Billion Range: Is Docking a Computational Alternative to DNA-Encoded Libraries? 8963-8979 2024 64 J. Chem. Inf. Model. 23 https://doi.org/10.1021/acs.jcim.4c00803 db/journals/jcisd/jcisd64.html#MihalovitsSBK24 streams/journals/jcisd

Tibor Viktor Szalai Dávid Bajusz Rita Börzsei Balázs Zoltán Zsidó Janez Ilas György G. Ferenczy Csaba Hetényi György M. Keserü Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments. 8980-8998 2024 64 J. Chem. Inf. Model. 23 https://doi.org/10.1021/acs.jcim.4c01291 db/journals/jcisd/jcisd64.html#SzalaiBBZIFHK24 streams/journals/jcisd

Gáspár Pándy-Szekeres Jimmy Caroli Alibek Mamyrbekov Ali A Kermani György M. Keserü Albert J. Kooistra David E. Gloriam GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources. 395-402 2023 January 51 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkac1013 db/journals/nar/nar51.html#PandySzekeresCMKKKG23

Dávid Bajusz Gáspár Pándy-Szekeres Ágnes Takács Elvin D. de araujo György M. Keserü SH2db, an information system for the SH2 domain. 542-552 2023 July 51 Nucleic Acids Res. W1 https://doi.org/10.1093/nar/gkad420 db/journals/nar/nar51.html#BajuszPTaK23

Amanda E. Wakefield Dávid Bajusz Dima Kozakov György M. Keserü Sandor Vajda Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. 4937-4954 2022 62 J. Chem. Inf. Model. 20 https://doi.org/10.1021/acs.jcim.2c00209 db/journals/jcisd/jcisd62.html#WakefieldBKKV22

Gáspár Pándy-Szekeres Mauricio Esguerra Alexander S. Hauser Jimmy Caroli Christian Munk Steven Pilger György M. Keserü Albert J. Kooistra David E. Gloriam The G protein database, GproteinDb. 518-525 2022 50 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkab852 db/journals/nar/nar50.html#Pandy-SzekeresE22

Andrea Scarpino László Petri Damijan Knez Tímea Imre Péter Ábrányi-Balogh György G. Ferenczy Stanislav Gobec György M. Keserü WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors. 223-244 2021 35 J. Comput. Aided Mol. Des. 2 https://doi.org/10.1007/s10822-020-00371-5 db/journals/jcamd/jcamd35.html#ScarpinoPKIAFGK21

Albert J. Kooistra Stefan Mordalski Gáspár Pándy-Szekeres Mauricio Esguerra Alibek Mamyrbekov Christian Munk György M. Keserü David E. Gloriam GPCRdb in 2021: integrating GPCR sequence, structure and function. D335-D343 2021 49 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkaa1080 https://www.wikidata.org/entity/Q104059988 db/journals/nar/nar49.html#KooistraMPEMMKG21

Anita Rácz György M. Keserü Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling. 831-839 2020 34 J. Comput. Aided Mol. Des. 8 https://doi.org/10.1007/s10822-020-00308-y https://www.wikidata.org/entity/Q90716418 db/journals/jcamd/jcamd34.html#RaczK20

Levente M. Mihalovits György G. Ferenczy György M. Keserü Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations. 6579-6594 2020 60 J. Chem. Inf. Model. 12 https://doi.org/10.1021/acs.jcim.0c00834 https://www.wikidata.org/entity/Q104138503 db/journals/jcisd/jcisd60.html#MihalovitsFK20

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. 6612-6623 2020 60 J. Chem. Inf. Model. 12 https://doi.org/10.1021/acs.jcim.0c00877 https://www.wikidata.org/entity/Q104132020 db/journals/jcisd/jcisd60.html#WakefieldYBCKKW20

Zoltán Orgován György G. Ferenczy György M. Keserü The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu5 receptor case study. 787-797 2019 33 J. Comput. Aided Mol. Des. 9 https://doi.org/10.1007/s10822-019-00224-w https://www.wikidata.org/entity/Q90203330 db/journals/jcamd/jcamd33.html#OrgovanFK19

Levente M. Mihalovits György G. Ferenczy György M. Keserü Catalytic Mechanism and Covalent Inhibition of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials. 5161-5173 2019 59 J. Chem. Inf. Model. 12 https://doi.org/10.1021/acs.jcim.9b00691 https://www.wikidata.org/entity/Q91245516 db/journals/jcisd/jcisd59.html#MihalovitsFK19

Zoltán Orgován György G. Ferenczy Thomas Steinbrecher Bence Szilágyi Dávid Bajusz György M. Keserü Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors. 331-345 2018 32 J. Comput. Aided Mol. Des. 2 https://doi.org/10.1007/s10822-018-0097-y https://www.wikidata.org/entity/Q47863372 db/journals/jcamd/jcamd32.html#OrgovanFSSBK18

Andrea Scarpino György G. Ferenczy György M. Keserü Comparative Evaluation of Covalent Docking Tools. 1441-1458 2018 58 J. Chem. Inf. Model. 7 https://doi.org/10.1021/acs.jcim.8b00228 https://www.wikidata.org/entity/Q89063656 db/journals/jcisd/jcisd58.html#ScarpinoFK18

Dávid Bajusz György G. Ferenczy György M. Keserü Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening. 234-247 2016 56 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.5b00634 https://www.wikidata.org/entity/Q55033983 db/journals/jcisd/jcisd56.html#BajuszFK16

Ádám A. Kelemen Robert Kiss György G. Ferenczy László Kovács Beáta Flachner Zsolt Lorincz György M. Keserü Structure-Based Consensus Scoring Scheme for Selecting Class A Aminergic GPCR Fragments. 412-422 2016 56 J. Chem. Inf. Model. 2 https://doi.org/10.1021/acs.jcim.5b00598 https://www.wikidata.org/entity/Q35892490 db/journals/jcisd/jcisd56.html#KelemenKFKFLK16

Ádám A. Kelemen György G. Ferenczy György M. Keserü A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands. 59-66 2015 29 J. Comput. Aided Mol. Des. 1 https://doi.org/10.1007/s10822-014-9804-5 https://www.wikidata.org/entity/Q35345510 db/journals/jcamd/jcamd29.html#KelemenFK15

Ádám A. Kelemen György G. Ferenczy György M. Keserü Erratum to: A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands. 67 2015 29 J. Comput. Aided Mol. Des. 1 https://doi.org/10.1007/s10822-014-9812-5 https://www.wikidata.org/entity/Q85959848 db/journals/jcamd/jcamd29.html#KelemenFK15a

Márton Vass Balázs Jójárt Ferenc Bogár Gábor Paragi György M. Keserü Ákos Tarcsay Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor. 1137-1149 2015 29 J. Comput. Aided Mol. Des. 12 https://doi.org/10.1007/s10822-015-9883-y https://www.wikidata.org/entity/Q86706640 db/journals/jcamd/jcamd29.html#VassJBPKT15

Ákos Tarcsay Gábor Paragi Márton Vass Balázs Jójárt Ferenc Bogár György M. Keserü The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs. 2990-2999 2013 53 J. Chem. Inf. Model. 11 https://doi.org/10.1021/ci400087b https://www.wikidata.org/entity/Q54781021 db/journals/jcisd/jcisd53.html#TarcsayPVJBK13

Márton Vass Ákos Tarcsay György M. Keserü Multiple ligand docking by Glide: implications for virtual second-site screening. 821-834 2012 26 J. Comput. Aided Mol. Des. 7 https://doi.org/10.1007/s10822-012-9578-6 https://www.wikidata.org/entity/Q84230608 db/journals/jcamd/jcamd26.html#VassTK12

Robert Kiss Mark Sandor Anikó Gere Éva Schmidt György Balogh Béla Kiss László Molnár Christian Lemmen György M. Keserü Discovery of Novel Histamine H4 and Serotonin Transporter Ligands Using the Topological Feature Tree Descriptor. 233-242 2012 52 J. Chem. Inf. Model. 1 https://doi.org/10.1021/ci2004972 https://www.wikidata.org/entity/Q34100724 db/journals/jcisd/jcisd52.html#KissSGSBKMLK12

György G. Ferenczy György M. Keserü Thermodynamics of Fragment Binding. 1039-1045 2012 52 J. Chem. Inf. Model. 4 https://doi.org/10.1021/ci200608b https://www.wikidata.org/entity/Q34212572 db/journals/jcisd/jcisd52.html#FerenczyK12

Ákos Tarcsay Robert Kiss György M. Keserü Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach. 399-408 2010 24 J. Comput. Aided Mol. Des. 5 https://doi.org/10.1007/s10822-010-9347-3 https://www.wikidata.org/entity/Q43111257 db/journals/jcamd/jcamd24.html#TarcsayKK10

Mark Sandor Robert Kiss György M. Keserü Virtual Fragment Docking by Glide: a Validation Study on 190 Protein-Fragment Complexes. 1165-1172 2010 50 J. Chem. Inf. Model. 6 https://doi.org/10.1021/ci1000407 https://www.wikidata.org/entity/Q84201192 db/journals/jcisd/jcisd50.html#SandorKK10

György G. Ferenczy György M. Keserü Enthalpic Efficiency of Ligand Binding. 1536-1541 2010 50 J. Chem. Inf. Model. 9 https://doi.org/10.1021/ci100125a https://www.wikidata.org/entity/Q84659355 db/journals/jcisd/jcisd50.html#FerenczyK10

Balázs Jójárt Robert Kiss Béla Viskolcz György M. Keserü Activation Mechanism of the Human Histamine H4 Receptor - An Explicit Membrane Molecular Dynamics Simulation Study. 1199-1210 2008 48 J. Chem. Inf. Model. 6 https://doi.org/10.1021/ci700450w https://www.wikidata.org/entity/Q40078321 db/journals/jcisd/jcisd48.html#JojartKVK08

Tímea Polgár Dóra K. Menyhárd György M. Keserü Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets. 539-548 2007 21 J. Comput. Aided Mol. Des. 9 https://doi.org/10.1007/s10822-007-9137-8 https://www.wikidata.org/entity/Q46932255 db/journals/jcamd/jcamd21.html#PolgarMK07

Tímea Polgár Csaba Magyar István Simon György M. Keserü Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1). 2366-2373 2007 47 J. Chem. Inf. Model. 6 https://doi.org/10.1021/ci700223p https://www.wikidata.org/entity/Q46943882 db/journals/jcisd/jcisd47.html#PolgarMSK07

Tímea Polgár György M. Keserü Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and beta-Secretase. 1795-1805 2006 46 J. Chem. Inf. Model. 4 https://doi.org/10.1021/ci050412x https://www.wikidata.org/entity/Q53746377 db/journals/jcisd/jcisd46.html#PolgarK06

György M. Keserü László Molnár METAPRINT: A Metabolic Fingerprint. Application to Cassette Design for High-Throughput ADME Screening. 437-444 2002 42 J. Chem. Inf. Comput. Sci. 2 https://doi.org/10.1021/ci010106t https://www.wikidata.org/entity/Q30827813 db/journals/jcisd/jcisd42.html#KeseruM02

György M. Keserü A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. 649-657 2001 15 J. Comput. Aided Mol. Des. 7 https://doi.org/10.1023/A:1011911204383 https://www.wikidata.org/entity/Q30760210 db/journals/jcamd/jcamd15.html#Keseru01

István Kolossváry György M. Keserü Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3. 21-30 2001 22 J. Comput. Chem. 1 https://doi.org/10.1002/1096-987X(20010115)22:1<21::AID-JCC3>3.0.CO;2-I db/journals/jcc/jcc22.html#KolossvaryK01

György M. Keserü László Molnár High-Throughput Prediction of Blood-Brain Partitioning: A Thermodynamic Approach. 120-128 2001 41 J. Chem. Inf. Comput. Sci. 1 https://doi.org/10.1021/ci000043z https://www.wikidata.org/entity/Q73508127 db/journals/jcisd/jcisd41.html#KeseruM01

Attila Kovács Gábor I. Csonka György M. Keserü Comparison of ab initio and density functional methods for vibrational analysis of TeCl4. 308-318 1998 19 J. Comput. Chem. 3 https://doi.org/10.1002/(SICI)1096-987X(199802)19:3<308::AID-JCC5>3.0.CO;2-X db/journals/jcc/jcc19.html#KovacsCK98

Péter Ábrányi-Balogh Elvin D. de araujo Dávid Bajusz György Balogh Dmitri Beglov Brian Joseph Bender Ferenc Bogár Rita Börzsei Giovanni Bottegoni Jimmy Caroli Marcelo Santos Castilho I-Jen Chen Simon Cross Gábor I. Csonka Mauricio Esguerra György G. Ferenczy Beáta Flachner Anikó Gere David E. Gloriam Stanislav Gobec Chris de Graaf Alexander S. Hauser Csaba Hetényi Janez Ilas Tímea Imre Balázs Jójárt Ádám A. Kelemen Ali A Kermani Béla Kiss Robert Kiss Damijan Knez István Kolossváry Albert J. Kooistra Attila Kovács László Kovács Dima Kozakov Christian Lemmen Zsolt Lorincz Csaba Magyar Alibek Mamyrbekov Dóra K. Menyhárd Levente M. Mihalovits László Molnár Stefan Mordalski Christian Munk Noel M. O'Boyle Zoltán Orgován Tommaso Palomba Gáspár Pándy-Szekeres Gábor Paragi Nikolett Péczka Sonja Peter László Petri Steven Pilger Tímea Polgár Anita Rácz Mark Sandor Andrea Scarpino Éva Schmidt István Simon Levente Sipos-Szabó Lydia Siragusa Thomas Steinbrecher Tibor Viktor Szalai Bence Szilágyi Ágnes Takács Ákos Tarcsay Morgan C. Thomas Sandor Vajda Márton Vass Béla Viskolcz Amanda E. Wakefield Adrian Whitty Christine Yueh Balázs Zoltán Zsidó