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For: Sarti E, Granata D, Seno F, Trovato A, Laio A. Native fold and docking pose discrimination by the same residue-based scoring function. Proteins 2015;83:621-30. [DOI: 10.1002/prot.24764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/15/2014] [Accepted: 12/31/2014] [Indexed: 11/10/2022]
Number Cited by Other Article(s)
1
Tandiana R, Barletta GP, Soler MA, Fortuna S, Rocchia W. Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions. J Chem Theory Comput 2024;20:2630-2642. [PMID: 38445482 DOI: 10.1021/acs.jctc.3c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
2
Soler MA, Minovski N, Rocchia W, Fortuna S. Replica-exchange optimization of antibody fragments. Comput Biol Chem 2023;103:107819. [PMID: 36657284 DOI: 10.1016/j.compbiolchem.2023.107819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/16/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
3
Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study. Comput Struct Biotechnol J 2023;21:1746-1758. [PMID: 36890879 PMCID: PMC9986244 DOI: 10.1016/j.csbj.2023.02.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023]  Open
4
Medagli B, Soler MA, De Zorzi R, Fortuna S. Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders. Methods Mol Biol 2023;2552:333-359. [PMID: 36346602 DOI: 10.1007/978-1-0716-2609-2_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
5
Bartuzi D, Kaczor AA, Matosiuk D. Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling. Methods Mol Biol 2023;2627:25-40. [PMID: 36959440 DOI: 10.1007/978-1-0716-2974-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
6
Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules. PLoS One 2022;17:e0254969. [PMID: 35085247 PMCID: PMC8794220 DOI: 10.1371/journal.pone.0254969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/28/2021] [Indexed: 11/19/2022]  Open
7
Soler MA, Medagli B, Semrau MS, Storici P, Bajc G, de Marco A, Laio A, Fortuna S. A consensus protocol for the in silico optimisation of antibody fragments. Chem Commun (Camb) 2019;55:14043-14046. [PMID: 31690899 DOI: 10.1039/c9cc06182g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
8
Ochoa R, Laio A, Cossio P. Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. J Chem Inf Model 2019;59:3464-3473. [PMID: 31290667 DOI: 10.1021/acs.jcim.9b00403] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
9
Battisti A, Zamuner S, Sarti E, Laio A. Toward a unified scoring function for native state discrimination and drug-binding pocket recognition. Phys Chem Chem Phys 2019;20:17148-17155. [PMID: 29900428 DOI: 10.1039/c7cp08170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
10
Soler MA, Fortuna S, de Marco A, Laio A. Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories. Phys Chem Chem Phys 2018;20:3438-3444. [PMID: 29328338 DOI: 10.1039/c7cp08116b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
11
Škrbić T, Zamuner S, Hong R, Seno F, Laio A, Trovato A. Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes. Proteins 2018;86:393-404. [DOI: 10.1002/prot.25454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/22/2017] [Accepted: 01/05/2018] [Indexed: 01/10/2023]
12
Sarti E, Gladich I, Zamuner S, Correia BE, Laio A. Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses. Proteins 2016;84:1312-20. [DOI: 10.1002/prot.25079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 12/28/2022]
13
Rigid-Docking Approaches to Explore Protein-Protein Interaction Space. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016;160:33-55. [PMID: 27830312 DOI: 10.1007/10_2016_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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