These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

172 related articles for article (PubMed ID: 31051038)

  • 1. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.
    Vangone A; Schaarschmidt J; Koukos P; Geng C; Citro N; Trellet ME; Xue LC; Bonvin AMJJ
    Bioinformatics; 2019 May; 35(9):1585-1587. PubMed ID: 31051038
    [TBL] [Abstract][Full Text] [Related]  

  • 2. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
    Xue LC; Rodrigues JP; Kastritis PL; Bonvin AM; Vangone A
    Bioinformatics; 2016 Dec; 32(23):3676-3678. PubMed ID: 27503228
    [TBL] [Abstract][Full Text] [Related]  

  • 3. PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes.
    Jiménez-García B; Elez K; Koukos PI; Bonvin AM; Vangone A
    Bioinformatics; 2019 Nov; 35(22):4821-4823. PubMed ID: 31141126
    [TBL] [Abstract][Full Text] [Related]  

  • 4. PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes.
    Vangone A; Bonvin AMJJ
    Bio Protoc; 2017 Feb; 7(3):e2124. PubMed ID: 34458447
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
    Kurkcuoglu Z; Koukos PI; Citro N; Trellet ME; Rodrigues JPGLM; Moreira IS; Roel-Touris J; Melquiond ASJ; Geng C; Schaarschmidt J; Xue LC; Vangone A; Bonvin AMJJ
    J Comput Aided Mol Des; 2018 Jan; 32(1):175-185. PubMed ID: 28831657
    [TBL] [Abstract][Full Text] [Related]  

  • 6. CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
    Pires DE; Ascher DB
    Nucleic Acids Res; 2016 Jul; 44(W1):W557-61. PubMed ID: 27151202
    [TBL] [Abstract][Full Text] [Related]  

  • 7. AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.
    Labbé CM; Pencheva T; Jereva D; Desvillechabrol D; Becot J; Villoutreix BO; Pajeva I; Miteva MA
    Nucleic Acids Res; 2017 Jul; 45(W1):W350-W355. PubMed ID: 28486703
    [TBL] [Abstract][Full Text] [Related]  

  • 8. The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.
    van Zundert GC; Trellet M; Schaarschmidt J; Kurkcuoglu Z; David M; Verlato M; Rosato A; Bonvin AM
    J Mol Biol; 2017 Feb; 429(3):399-407. PubMed ID: 27939290
    [TBL] [Abstract][Full Text] [Related]  

  • 9. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.
    Konc J; Miller BT; Štular T; Lešnik S; Woodcock HL; Brooks BR; Janežič D
    J Chem Inf Model; 2015 Nov; 55(11):2308-14. PubMed ID: 26509288
    [TBL] [Abstract][Full Text] [Related]  

  • 10. LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.
    Xie ZR; Liu CK; Hsiao FC; Yao A; Hwang MJ
    Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W292-6. PubMed ID: 23609546
    [TBL] [Abstract][Full Text] [Related]  

  • 11. FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins.
    Roche DB; Tetchner SJ; McGuffin LJ
    BMC Bioinformatics; 2011 May; 12():160. PubMed ID: 21575183
    [TBL] [Abstract][Full Text] [Related]  

  • 12. The FunFOLD2 server for the prediction of protein-ligand interactions.
    Roche DB; Buenavista MT; McGuffin LJ
    Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W303-7. PubMed ID: 23761453
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
    Deng N; Flynn WF; Xia J; Vijayan RS; Zhang B; He P; Mentes A; Gallicchio E; Levy RM
    J Comput Aided Mol Des; 2016 Sep; 30(9):743-751. PubMed ID: 27562018
    [TBL] [Abstract][Full Text] [Related]  

  • 14. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.
    Konc J; Janežič D
    Nucleic Acids Res; 2014 Jul; 42(Web Server issue):W215-20. PubMed ID: 24861616
    [TBL] [Abstract][Full Text] [Related]  

  • 15. FRODOCK 2.0: fast protein-protein docking server.
    Ramírez-Aportela E; López-Blanco JR; Chacón P
    Bioinformatics; 2016 Aug; 32(15):2386-8. PubMed ID: 27153583
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3.
    Kumar A; Zhang KYJ
    J Comput Aided Mol Des; 2019 Jan; 33(1):47-59. PubMed ID: 30084081
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A web server for analysis, comparison and prediction of protein ligand binding sites.
    Singh H; Srivastava HK; Raghava GP
    Biol Direct; 2016 Mar; 11(1):14. PubMed ID: 27016210
    [TBL] [Abstract][Full Text] [Related]  

  • 18. PESDserv: a server for high-throughput comparison of protein binding site surfaces.
    Das S; Krein MP; Breneman CM
    Bioinformatics; 2010 Aug; 26(15):1913-4. PubMed ID: 20538727
    [TBL] [Abstract][Full Text] [Related]  

  • 19. PatchSearch: a web server for off-target protein identification.
    Rey J; Rasolohery I; Tufféry P; Guyon F; Moroy G
    Nucleic Acids Res; 2019 Jul; 47(W1):W365-W372. PubMed ID: 31131411
    [TBL] [Abstract][Full Text] [Related]  

  • 20. SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.
    Rueda M; Katritch V; Raush E; Abagyan R
    Bioinformatics; 2010 Nov; 26(21):2784-5. PubMed ID: 20871105
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.