- Products
- Publications in PUBMED using FoldX
2023
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Hajihassan Z, Afsharian NPesaran, Ansari-Pour N. "In silico engineering a CD80 variant with increased affinity to CTLA-4 and decreased affinity to CD28 for optimized cancer immunotherapy." J Immunol Methods. 2023;513:113425.
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M DDarshan V, Sivaramakrishnan V, K Kumar A. "Structural systems biology approach delineate the functional implications of SNPs in exon junction complex interaction network." J Biomol Struct Dyn. 2023:1-18.
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Koşaca M, Yılmazbilek İ, Karaca E. "PROT-ON: A structure-based detection of designer PROTein interface MutatiONs." Front Mol Biosci. 2023;10:1063971.
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Montero-Blay A, Blanco JDelgado, Rodriguez-Arce I, et al. "Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation." Mol Syst Biol. 2023;19(1):e11037.
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Le J, Min J-H. "Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein." J Biomol Struct Dyn. 2023:1-28.
2022
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Cui H, Davari MD, Schwaneberg U. "Recombination of Single Beneficial Substitutions Obtained from Protein Engineering by Computer-Assisted Recombination (CompassR)." Methods Mol Biol. 2022;2461:9-18.
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Hasnain MJawad Ul, Amin F, Ghani A, et al. "Structural and Functional Impact of Damaging Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) on Human VPS35 Protein Using Computational Approaches." IEEE/ACM Trans Comput Biol Bioinform. 2022;19(6):3715-3724.
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García-Cebollada H, López A, Sancho J. "Protposer: The web server that readily proposes protein stabilizing mutations with high PPV." Comput Struct Biotechnol J. 2022;20:2415-2433.
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Van Der Kant R, Louros N, Schymkowitz J, Rousseau F. "Thermodynamic analysis of amyloid fibril structures reveals a common framework for stability in amyloid polymorphs." Structure. 2022;30(8):1178-1189.e3.
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Standley M, Blay V, Guthrie VBeleva, et al. "Experimental and Analysis of TEM β-Lactamase Adaptive Evolution." ACS Infect Dis. 2022;8(12):2451-2463.
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Zhang B, Lü C, Zhang M, Xu F. "[Improving the thermal stability of lipase based on multiple computational design strategies]." Sheng Wu Gong Cheng Xue Bao. 2022;38(4):1537-1553.
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Radusky LG, Serrano L. "pyFoldX: enabling biomolecular analysis and engineering along structural ensembles." Bioinformatics. 2022;38(8):2353-2355.
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Beach SS, Hull MKA, F Ytreberg M, Patel JSuresh, Miura TA. "Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein." J Virol. 2022;96(13):e0035322.
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Wang Y, Li C, Ban X, et al. "Disulfide Bond Engineering for Enhancing the Thermostability of the Maltotetraose-Forming Amylase from STB07." Foods. 2022;11(9).
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Liu Y-Y, Lin I-C, Chen P-C, Lee C-C, Meng M. "Crystal structure of a Burkholderia peptidase and modification of the substrate-binding site for enhanced hydrolytic activity toward gluten-derived pro-immunogenic peptides." Int J Biol Macromol. 2022;222(Pt B):2258-2269.
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Barnes JE, Lund-Andersen PK, Patel JSuresh, F Ytreberg M. "The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6." Sci Rep. 2022;12(1):18819.
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Li S, Patel JSuresh, Yang J, et al. "Defining the HIV Capsid Binding Site of Nucleoporin 153." mSphere. 2022;7(5):e0031022.
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Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, M Tricerri A. "Evolutionary and structural constraints influencing apolipoprotein A-I amyloid behavior." Proteins. 2022;90(1):258-269.
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Pak MA, Ivankov DN. "Best templates outperform homology models in predicting the impact of mutations on protein stability." Bioinformatics. 2022;38(18):4312-4320.
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Tiberti M, Terkelsen T, Degn K, et al. "MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles." Brief Bioinform. 2022;23(3).
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Dolgikh B, Woldring D. "Site-wise Diversification of Combinatorial Libraries Using Insights from Structure-guided Stability Calculations." Methods Mol Biol. 2022;2491:63-73.
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Martín M, Brunello FG, Modenutti CP, Nicola JP, Marti MA. "MotSASi: Functional short linear motifs (SLiMs) prediction based on genomic single nucleotide variants and structural data." Biochimie. 2022;197:59-73.
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Yasuda S, Akiyama T, Kojima K, et al. "Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations." J Phys Chem B. 2022;126(5):1004-1015.
2021
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Zhang C, Codina N, Tang J, et al. "Comparison of the pH- and thermally-induced fluctuations of a therapeutic antibody Fab fragment by molecular dynamics simulation." Comput Struct Biotechnol J. 2021;19:2726-2741.
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Vera AManuel, Galera-Prat A, Wojciechowski M, et al. "Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization." Structure. 2021;29(6):587-597.e8.
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Wu X, Craik DJ, Kaas Q. "Interactions of Globular and Ribbon [γ4E]GID with α4β2 Neuronal Nicotinic Acetylcholine Receptor." Mar Drugs. 2021;19(9).
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Dutta K, Elmezayen AD, Al-Obaidi A, et al. "Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations." J Mol Struct. 2021;1246:131113.
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Yang P-K, Liang X-Y, Lin M, et al. "Population genetic analysis of the Plasmodium falciparum erythrocyte binding antigen-175 (EBA-175) gene in Equatorial Guinea." Malar J. 2021;20(1):374.
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Ying Y, Hong X, Xu X, et al. "Mechanism evaluation for an amino acid substitution p.Y246C of B-glycosyltransferase enzyme with Bweak phenotype." Vox Sang. 2021;116(4):464-470.
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Kochhar A, Khan NSaba, Deval R, et al. "Protein-protein interaction and in silico mutagenesis studies on IL17A and its peptide inhibitor." 3 Biotech. 2021;11(6):305.
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Petrosino M, Novak L, Pasquo A, et al. "Analysis and Interpretation of the Impact of Missense Variants in Cancer." Int J Mol Sci. 2021;22(11).
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Bi J, Jing X, Wu L, et al. "Computational design of noncanonical amino acid-based thioether staples at N/C-terminal domains of multi-modular pullulanase for thermostabilization in enzyme catalysis." Comput Struct Biotechnol J. 2021;19:577-585.
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Bahia MSingh, Khazanov N, Zhou Q, et al. "Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator." J Chem Inf Model. 2021;61(4):1762-1777.
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Armaghan F, Hajihassan Z. "Engineering a variant of IL-17RA with high binding affinity to IL-17A for optimized immunotherapy." Biotechnol Rep (Amst). 2021;32:e00682.
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Zhao Y, Li D, Bai X, et al. "Improved thermostability of proteinase K and recognizing the synergistic effect of Rosetta and FoldX approaches." Protein Eng Des Sel. 2021;34.
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Junk P, Kiel C. "Engineering of Biological Pathways: Complex Formation and Signal Transduction." Methods Mol Biol. 2021;2315:59-70.
2020
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Cianferoni D, Radusky LG, Head SA, Serrano L, Delgado J. "ProteinFishing: a protein complex generator within the ModelX toolsuite." Bioinformatics. 2020;36(14):4208-4210.
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Kalman ZE, Mészáros B, Gáspári Z, Dobson L. "Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region." Sci Rep. 2020;10(1):17333.
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Bi J, Chen S, Zhao X, Nie Y, Xu Y. "Computation-aided engineering of starch-debranching pullulanase from Bacillus thermoleovorans for enhanced thermostability." Appl Microbiol Biotechnol. 2020;104(17):7551-7562.
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S UKumar, R B, D TKumar, C Doss GPriya, Zayed H. "Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach." J Biomol Struct Dyn. 2020:1-15.
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M Rahman S, M Islam R, Alam ASMRubaye, et al. "Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein and its consequences." J Med Virol. 2020.
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Wang R, Wang S, Xu Y, Yu X. "Enhancing the thermostability of Rhizopus chinensis lipase by rational design and MD simulations." Int J Biol Macromol. 2020;160:1189-1200.
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Choudhuri KSankar Roy, Mishra S. "Structural basis of BMP-2 and BMP-7 interactions with antagonists Gremlin-1 and Noggin in Glioblastoma tumors." J Comput Chem. 2020.
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Rasafar N, Barzegar A, Aghdam EMehdizadeh. "Design and development of high affinity dual anticancer peptide-inhibitors against p53-MDM2/X interaction." Life Sci. 2020;245:117358.
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Zhang N, Lu H, Chen Y, et al. "PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions." Int J Mol Sci. 2020;21(15).
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Yang J, Naik N, Patel JSuresh, et al. "Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness." PLoS One. 2020;15(5):e0233509.
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Amengual-Rigo P, Fernández-Recio J, Guallar V. "UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes." Bioinformatics. 2020.
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Othman H, Bouslama Z, Brandenburg J-T, et al. "Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism." Biochem Biophys Res Commun. 2020;527(3):702-708.
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Gonzalez TR, Martin KP, Barnes JE, Patel JSuresh, F Ytreberg M. "Assessment of software methods for estimating protein-protein relative binding affinities." PLoS One. 2020;15(12):e0240573.
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Chitongo R, Obasa AEmmanuel, Mikasi SGiven, Jacobs GBrendon, Cloete R. "Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding." PLoS One. 2020;15(5):e0223464.
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Chen F, Chen X, Jiang F, et al. "Computational analysis of androgen receptor (AR) variants to decipher the relationship between protein stability and related-diseases." Sci Rep. 2020;10(1):12101.
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"PDBe-KB: a community-driven resource for structural and functional annotations." Nucleic Acids Res. 2020;48(D1):D344-D353.
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Huang P, Chu SKS, Frizzo HN, Connolly MP, Caster RW, Siegel JB. "Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset." ACS Omega. 2020;5(12):6487-6493.
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Karthikeyan V, Vickram AS, Manian R. "Estimation of varicocele associated human ARG2 and NOS1 proteins and computational analysis on the effect of its nsSNPs." Int J Biol Macromol. 2020;164:735-747.
2019
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Fang X, Huang J, Zhang R, et al. "Convolution Neural Network-Based Prediction of Protein Thermostability." J Chem Inf Model. 2019.
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Yadegari F, Majidzadeh K. "In silico analysis for determining the deleterious nonsynonymous single nucleotide polymorphisms of genes." Mol Biol Res Commun. 2019;8(4):141-150.
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Strokach A, Corbi-Verge C, Kim PM. "Predicting changes in protein stability caused by mutation using sequence-and structure-based methods in a CAGI5 blind challenge." Hum. Mutat.. 2019;40(9):1414-1423.
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Scheps KG, Hasenahuer MA, Parisi G, Targovnik HM, Fornasari MS. "Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis." Hum. Mutat.. 2019.
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Khan A, Junaid M, Li C-D, et al. "Dynamics Insights Into the Gain of Flexibility by Helix-12 in ESR1 as a Mechanism of Resistance to Drugs in Breast Cancer Cell Lines." Front Mol Biosci. 2019;6:159.
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Shang X, Nelson DC. "Contributions of Net Charge on the PlyC Endolysin CHAP Domain." Antibiotics (Basel). 2019;8(2).
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Cui H, Cao H, Cai H, Karl-Erich J, Davari MDolatabadi, Schwaneberg U. "Computer-assisted Recombination (CompassR) teaches us how to recombine beneficial substitutions from directed evolution campaigns." Chemistry. 2019.
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Reyes-Espinosa F, Juárez-Saldivar A, Palos I, Herrera-Mayorga V, García-Pérez C, Rivera G. "In Silico Analysis of Homologous Heterodimers of Cruzipain-Chagasin from Structural Models Built by Homology." Int J Mol Sci. 2019;20(6).
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Yu T-G, Kim H-S, Choi Y. "B-SIDER: Computational Algorithm for the Design of Complementary β-Sheet Sequences." J Chem Inf Model. 2019;59(10):4504-4511.
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Blanco JDelgado, Radusky LG, Cianferoni D, Serrano L. "Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX." Proc. Natl. Acad. Sci. U.S.A.. 2019.
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Delgado J, Radusky LG, Cianferoni D, Serrano L. "FoldX 5.0: working with RNA, small molecules and a new graphical interface." Bioinformatics. 2019;35(20):4168-4169.
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Peng M, Maier M, Esch J, Schug A, Rabe KS. "Direct coupling analysis improves the identification of beneficial amino acid mutations for the functional thermostabilization of a delicate decarboxylase." Biol. Chem.. 2019;400(11):1519-1527.
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Zandsalimi F, Hajihassan Z, Hamidi R. "Denovo designing: a novel signal peptide for tat translocation pathway to transport activin A to the periplasmic space of E. coli." Biotechnol. Lett.. 2019.
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Singh S, Choudhary S, Anand V, et al. "New insights into the catalytic inactivity of mammary gland protein-40, a chitinase-like protein expressed during mammary gland involution." Mol. Biol. Rep.. 2019;46(2):2243-2257.
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Kueppers F, Andrake MD, Xu Q, Dunbrack RL, Kim J, Sanders CL. "Protein modeling to assess the pathogenicity of rare variants of SERPINA1 in patients suspected of having Alpha 1 Antitrypsin Deficiency." BMC Med. Genet.. 2019;20(1):125.
2018
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oštarić NŠ, O'Reilly FJ, Giansanti P, Heck AJR, Gavin A-C, van Noort V. "Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes." Mol. Cell Proteomics. 2018;17(12):2387-2401.
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Radusky L, Modenutti C, Delgado J, et al. "VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants." Front Genet. 2018;9:620.
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Sumbalova L, Stourac J, Martinek T, Bednar D, Damborsky J. "HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information." Nucleic Acids Res.. 2018;46(W1):W356-W362.
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Yenenler A, Venturini A, Burduroglu HCahit, Sezerman OUğur. "Investigating the structural properties of the active conformation BTL2 of a lipase from Geobacillus thermocatenulatus in toluene using molecular dynamic simulations and engineering BTL2 via in-silico mutation." J Mol Model. 2018;24(9):229.
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Buß O, Muller D, Jager S, Rudat J, Rabe KS. "Improvement in the Thermostability of a β-Amino Acid Converting ω-Transaminase by Using FoldX." Chembiochem. 2018;19(4):379-387.
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Hutapea HMartogi Lo, Maladan Y. "Relationship between HIV integrase polymorphisms and integrase inhibitor susceptibility: An analysis." Heliyon. 2018;4(12):e00956.
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Blanco JDelgado, Radusky L, Climente-González H, Serrano L. "FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1)." Nucleic Acids Res.. 2018.
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Usmanova DR, Bogatyreva NS, Bernad JAriño, et al. "Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation." Bioinformatics. 2018.
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Ang T-F, Salleh ABakar, Normi YM, Leow TChor. "In silico design of potentially functional artificial metallo-haloalkane dehalogenase containing catalytic zinc." 3 Biotech. 2018;8(7):314.
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Carleton LA, Chakravarthy R, van der Sloot AM, et al. "Generation of rationally-designed nerve growth factor (NGF) variants with receptor specificity." Biochem. Biophys. Res. Commun.. 2018;495(1):700-705.
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Khan NSaba, Verma R, Pradhan D, et al. "Analysis of interleukin 23 and 7G10 interactions for computational design of lead antibodies against immune-mediated inflammatory diseases." J. Recept. Signal Transduct. Res.. 2018;38(4):327-334.
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Wojciechowski M, Różycki B, Huy PDinh Quoc, Li MSuan, Bayer EA, Cieplak M. "Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module." Sci Rep. 2018;8(1):5051.
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Choi Y, Furlon JM, Amos RB, Griswold KE, Bailey-Kellogg C. "DisruPPI: structure-based computational redesign algorithm for protein binding disruption." Bioinformatics. 2018;34(13):i245-i253.
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Azadi S, Tafazzoli-Shadpour M, Omidvar R. "[Steered Molecular Dynamics Simulation Study of Quantified Effects of Point Mutation Induced by Breast Cancer on Mechanical Behavior of E-Cadherin]." Mol. Biol. (Mosk.). 2018;52(5):836-845.
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Anyndita NVeronica M, Dluha N, Rifa'i M, Himmah K, Wahyuningsih MDwi. "Designing and overproducing a tandem epitope of gp350/220 that shows a potential to become an EBV vaccine." Heliyon. 2018;4(3):e00564.
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Okumura A, Maruyama K, Shibata M, et al. "A patient with a GNAO1 mutation with decreased spontaneous movements, hypotonia, and dystonic features." Brain Dev.. 2018.
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Buß O, Rudat J, Ochsenreither K. "FoldX as Protein Engineering Tool: Better Than Random Based Approaches?" Comput Struct Biotechnol J. 2018;16:25-33.
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Goethe M, Gleixner J, Fita I, J Rubi M. "Prediction of Protein Configurational Entropy (Popcoen)." J Chem Theory Comput. 2018;14(3):1811-1819.
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Rojas-Rengifo DF, Alvarez-Silva MCamila, Ulloa-Guerrero CP, et al. "Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains' pathogenicity level." Comput Biol Chem. 2018;76:17-22.
2017
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Carlin DAlexander, Hapig-Ward S, Chan BWayne, et al. "Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed." PLoS ONE. 2017;12(5):e0176255.
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Gapsys V, de Groot BL. "Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes." J Chem Theory Comput. 2017;13(12):6275-6289.
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Nosrati M, Solbak S, Nordesjö O, et al. "Insights from engineering the Affibody-Fc interaction with a computational-experimental method." Protein Eng. Des. Sel.. 2017;30(9):593-601.
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Li L, Ye Y, Sang P, et al. "Effect of R119G Mutation on Human P5CR1 Dynamic Property and Enzymatic Activity." Biomed Res Int. 2017;2017:4184106.
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Jones BJ, Lim HYee, Huang J, Kazlauskas RJ. "Comparison of Five Protein Engineering Strategies for Stabilizing an α/β-Hydrolase." Biochemistry. 2017;56(50):6521-6532.
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Xiong P, Zhang C, Zheng W, Zhang Y. "BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts." J. Mol. Biol.. 2017;429(3):426-434.
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Kumar V, Rahman S, Choudhry H, et al. "Computing disease-linked SOD1 mutations: deciphering protein stability and patient-phenotype relations." Sci Rep. 2017;7(1):4678.
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Tomar JSingh, Peddinti RKrishna. "A. baumannii histone acetyl transferase Hpa2: optimization of homology modeling, analysis of protein-protein interaction and virtual screening." J. Biomol. Struct. Dyn.. 2017;35(5):1115-1126.
2016
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Tomar JSingh, Peddinti RKrishna. "Optimized method for TAG protein homology modeling: In silico and experimental structural characterization." Int. J. Biol. Macromol.. 2016;88:102-12.
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Sulea T, Vivcharuk V, Corbeil CR, Deprez C, Purisima EO. "Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities." J Chem Inf Model. 2016;56(7):1292-303.
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Miller CR, Johnson EL, Burke AZ, et al. "Initiating a watch list for Ebola virus antibody escape mutations." PeerJ. 2016;4:e1674.
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Van Durme J, De Baets G, Van Der Kant R, et al. "Solubis: a webserver to reduce protein aggregation through mutation." Protein Eng. Des. Sel.. 2016;29(8):285-9.
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Luo X-J, Zhao J, Li C-X, et al. "Combinatorial evolution of phosphotriesterase toward a robust malathion degrader by hierarchical iteration mutagenesis." Biotechnol. Bioeng.. 2016;113(11):2350-7.
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Nygaard M, Terkelsen T, Olsen AVidas, et al. "The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer." Front Mol Biosci. 2016;3:78.
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Sirin S, Apgar JR, Bennett EM, Keating AE. "AB-Bind: Antibody binding mutational database for computational affinity predictions." Protein Sci.. 2016;25(2):393-409.
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Huwe PJ, Xu Q, Shapovalov MV, Modi V, Andrake MD, Dunbrack RL. "Biological function derived from predicted structures in CASP11." Proteins. 2016;84 Suppl 1:370-91.
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Kowalsky CA, Whitehead TA. "Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing." Proteins. 2016;84(12):1914-1928.
2015
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Singh I, Nunia V, Sharma R, et al. "Mutational analysis of telomere complex genes in Indian population with acquired aplastic anemia." Leuk. Res.. 2015.
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Hashmi I, Shehu A. "idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking." J. Comput. Biol.. 2015;22(9):806-22.
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erný JČ, Biedermannová L, Mikulecký P, et al. "Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction: interferon- γ receptor 1 as a model." Biomed Res Int. 2015;2015:716945.
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Liu Q, Ren J, Song J, Li J. "Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots." PLoS ONE. 2015;10(12):e0144486.
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Heselpoth RD, Yin Y, Moult J, Nelson DC. "Increasing the stability of the bacteriophage endolysin PlyC using rationale-based FoldX computational modeling." Protein Eng. Des. Sel.. 2015;28(4):85-92.
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Yu H, Wang M-jun, Xuan N-xia, Shang Z-cai, Wu J. "Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides." J Zhejiang Univ Sci B. 2015;16(10):883-96.
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Wettstein S, Underhaug J, Perez B, et al. "Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria." Eur. J. Hum. Genet.. 2015;23(3):302-9.
2014
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McKeone R, Wikstrom M, Kiel C, Rakoczy EP. "Assessing the correlation between mutant rhodopsin stability and the severity of retinitis pigmentosa." Mol. Vis.. 2014;20:183-99.
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Liu Q, Hoi SCH, Kwoh CKeong, Wong L, Li J. "Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots." BMC Bioinformatics. 2014;15:57.
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Kiel C, Serrano L. "Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations." Mol. Syst. Biol.. 2014;10:727.
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Xi Y, Wu X, Gao L, et al. "Improving the anti-toxin abilities of the CMG2-Fc fusion protein with the aid of computational design." PLoS ONE. 2014;9(8):e104674.
2011
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Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J, Rousseau F. "A graphical interface for the FoldX forcefield." Bioinformatics. 2011;27(12):1711-2.
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Verschueren E, Vanhee P, van der Sloot AM, Serrano L, Rousseau F, Schymkowitz J. "Protein design with fragment databases." Curr. Opin. Struct. Biol.. 2011;21(4):452-9.
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Vanhee P, Verschueren E, Baeten L, et al. "BriX: a database of protein building blocks for structural analysis, modeling and design." Nucleic Acids Res.. 2011;39(Database issue):D435-42.
2007
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Kiel C, Foglierini M, Kuemmerer N, Beltrao P, Serrano L. "A genome-wide Ras-effector interaction network." J. Mol. Biol.. 2007;370(5):1020-32.
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Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS. "The stability effects of protein mutations appear to be universally distributed." J. Mol. Biol.. 2007;369(5):1318-32.
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Szczepek M, Brondani V, Büchel J, Serrano L, Segal DJ, Cathomen T. "Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases." Nat. Biotechnol.. 2007;25(7):786-93.
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Pey AL, Stricher F, Serrano L, Martinez A. "Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases." Am. J. Hum. Genet.. 2007;81(5):1006-24.
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Kölsch V, Seher T, Fernandez-Ballester GJ, Serrano L, Leptin M. "Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2." Science. 2007;315(5810):384-6.
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Kiel C, Serrano L. "Prediction of Ras-effector interactions using position energy matrices." Bioinformatics. 2007;23(17):2226-30.
2006
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Arnould S, Chames P, Perez C, et al. "Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets." J. Mol. Biol.. 2006;355(3):443-58.
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van der Sloot AM, Tur V, Szegezdi E, et al. "Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor." Proc. Natl. Acad. Sci. U.S.A.. 2006;103(23):8634-9.
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Musi V, Birdsall B, Fernandez-Ballester G, et al. "New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae." Protein Sci.. 2006;15(4):795-807.
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Kiel C, Serrano L. "The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes." J. Mol. Biol.. 2006;355(4):821-44.
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Kempkens O, Médina E, Fernandez-Ballester G, et al. "Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6." Eur. J. Cell Biol.. 2006;85(8):753-67.
2005
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Schymkowitz JWH, Rousseau F, Martins IC, Ferkinghoff-Borg J, Stricher F, Serrano L. "Prediction of water and metal binding sites and their affinities by using the Fold-X force field." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(29):10147-52.
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Kiel C, Wohlgemuth S, Rousseau F, et al. "Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations." J. Mol. Biol.. 2005;348(3):759-75.
-
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. "The FoldX web server: an online force field." Nucleic Acids Res.. 2005;33(Web Server issue):W382-8.
-
Wohlgemuth S, Kiel C, Krämer A, Serrano L, Wittinghofer F, Herrmann C. "Recognizing and defining true Ras binding domains I: biochemical analysis." J. Mol. Biol.. 2005;348(3):741-58.