Cited by 2,759Protein Structure and DynamicsEnzyme Structure and FunctionRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.

The FoldX web server: an online force field

Open access

Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., Serrano, L.·2005·Nucleic Acids Research

Open this paper in CoChat — free account Open PDF

Abstract

FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at http://foldx.embl.de/. The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gki387

Cites

23 of 23 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling
Guex, N., & Peitsch, M. C. (1997) · Electrophoresis · doi:10.1002/elps.1150181505 · Cited by 11,312 · cited 1×
“Although the pdb-reader in FoldX is continually extended to handle more exceptions, standardizing the format of anomalous ﬁles most often solves the problem—this can easily be achieved by opening and saving the ﬁle using Swiss PDB viewer (14) or WHATIF (15).”
Method
The interpretation of protein structures: Estimation of static accessibility
Lee, B., & Richards, F. M. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90324-x · Cited by 5,884 · cited 1×
“The occupancy of an atom i, Occ(i), is calculated using an envelope function (21) with a distance cut-off of 6 s (9).”
Method
WHAT IF: A molecular modeling and drug design program
Vriend, G. (1990) · Journal of Molecular Graphics · doi:10.1016/0263-7855(90)80070-v · Cited by 3,476 · cited 1×
“Although the pdb-reader in FoldX is continually extended to handle more exceptions, standardizing the format of anomalous ﬁles most often solves the problem—this can easily be achieved by opening and saving the ﬁle using Swiss PDB viewer (14) or WHATIF (15).”
Method
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
Guerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728 · cited 3×
“In addition, those water molecules that have a persistent interaction with groups of the protein, i.e. make more than two hydrogen bonds with the protein, are calculated explicitly in the D G wb term (8,9).”
BackgroundMethodInfluentialSelf-citation
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
Fernández‐Escamilla, A. M., Rousseau, F., Schymkowitz, J. W. H., & Serrano, L. G. (2004) · Nature Biotechnology · doi:10.1038/nbt1012 · Cited by 1,667 · cited 1×
“In this fashion, TANGO predicts correctly both the disease causing and protective mutations in a wide range of proteins including Alzheimers’ A b peptide, lysozyme and transthyretin (12).”
BackgroundSelf-citation
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
Abagyan, R. A., & Totrov, M. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1052 · Cited by 982 · cited 8×
“The statistical mechanics algorithm TANGO, publicly available at http:// TANGO.embl.de/, provides such a predictive model.”
MethodInfluential
Molecular basis for amyloid fibril formation and stability
Makin, O. S., Atkins, E. D. T., Sikorski, P., Johansson, J., & Serpell, L. C. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406847102 · Cited by 649 · cited 1×
“For protein aggregation no such detail is available, although recently the ﬁrst ever crystal structure of an amyloid ﬁbre was released (23).”
Background
Effective energy functions for protein structure prediction
Lazaridis, T. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00063-4 · Cited by 445 · cited 1×
“These are designated by Lazaridis and Karplus (1) as statistical (SEEF) and physical (PEEF) effective energy functions, respectively.”
Background
Protein-misfolding diseases: Getting out of shape
Dobson, C. M. (2002) · Nature · doi:10.1038/418729a · Cited by 341 · cited 1×
“The crystal structure conﬁrms the widespread observation in the ﬁeld that protein aggregates are generally rich in cross-beta structure (24), which allows a low-resolution structural approach to predict protein aggregation.”
Background
Rational design of faster associating and tighter binding protein complexes.
Schreiber, G., Selzer, T., & Albeck, S. (2000) · Nature Structural Biology · doi:10.1038/76744 · Cited by 299 · cited 1×
“(10), which was shown to give a good estimation of the association rate ( k on ) of complex formation.”
Background

Flagged first, then by citations

Show all 23 references

Sorted by citations

Items 801–900 of 1,005

Engineering of enzymes using non-natural amino acids
Li, Y., & Dalby, P. A. (2022) · Bioscience Reports · doi:10.1042/bsr20220168 · Cited by 24
Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations
Bai, Z., Wang, J., Li, J., Yuan, H., Wang, P., Zhang, M., Feng, Y., Cao, X., Cao, X., Kang, G., et al. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.12.021 · Cited by 24
Molecular damage in F abry disease: Characterization and prediction of alpha‐galactosidase A pathological mutations
Riera, C., Lois, S., Domı́nguez, C., Fernández‐Cadenas, I., Montaner, J., Rodríguez‐Sureda, V., & de la Cruz, X. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24708 · Cited by 24
A rational free energy-based approach to understanding and targeting disease-causing missense mutations
Zhang, Z., Witham, S., Petukh, M., et al. (2013) · Journal of the American Medical Informatics Association · doi:10.1136/amiajnl-2012-001505 · Cited by 24
Structural Insights into Saccharomyces cerevisiae Msh4–Msh5 Complex Function Using Homology Modeling
Rakshambikai, R., Srinivasan, N., & Nishant, K. T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078753 · Cited by 24
Hotspots in an Obligate Homodimeric Anticancer Target. Structural and Functional Effects of Interfacial Mutations in Human Thymidylate Synthase
Salo‐Ahen, O. M. H., Tochowicz, A., Pozzi, C., Cardinale, D., Ferrari, S., Boum, Y., Mangani, S., Stroud, R. M., Saxena, P., Myllykallio, H., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00137 · Cited by 24
Crystal Structure of a TSH Receptor Monoclonal Antibody: Insight Into Graves' Disease Pathogenesis
Chen, C., Hubbard, P. A., Salazar, L. M., McLachlan, S. M., Murali, R., & Rapoport, B. (2014) · Molecular Endocrinology · doi:10.1210/me.2014-1257 · Cited by 24
Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from C lostridium thermocellum and C lostridium cellulolyticum using deep sequencing
Kowalsky, C. A., & Whitehead, T. A. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25175 · Cited by 24
Structural modeling of a novel SLC 38A8 mutation that causes foveal hypoplasia
Toral, M. A., Velez, G., Boudreault, K., et al. (2017) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.266 · Cited by 24
Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods
Arora, S., Huwe, P. J., Sikder, R. K., Shah, M., Browne, A. J., Lesh, R. W., Nicolas, É., Deshpande, S., Hall, M. J., Dunbrack, R. L., et al. (2017) · Cancer Biology & Therapy · doi:10.1080/15384047.2017.1326439 · Cited by 26
A recurrent de novo mutation inACTG1causes isolated ocular coloboma
Rainger, J., Williamson, K. A., Soares, D. C., et al. (2017) · Human Mutation · doi:10.1002/humu.23246 · Cited by 24
Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access
Subramanian, K., Góra, A., Spruijt, R. B., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198990 · Cited by 24
AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation
Rawat, P., Prabakaran, R., Kumar, S., & Gromiha, M. M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz764 · Cited by 25
Structure of the Human ACP-ISD11 Heterodimer
Herrera, M. G., Noguera, M. E., Sewell, K. E., Suárez, W. A. A., Capece, L., Klinke, S., & Santos, J. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00539 · Cited by 24
HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae
Vedithi, S. C., Malhotra, S., Skwark, M. J., Munir, A., Acebrón-García-de-Eulate, M., Waman, V., Alsulami, A. F., Ascher, D. B., & Blundell, T. L. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.013 · Cited by 25
Dominant clade‐featured SARS‐CoV‐2 co‐occurring mutations reveal plausible epistasis: An in silico based hypothetical model
Alam, A. S. M. R. U., Islam, O. K., Hasan, M. S., Islam, M. R., Mahmud, S., Al‐Emran, H. M., Jahid, I. K., Crandall, K. A., & Hossain, M. A. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27416 · Cited by 24
Semi-Rational Engineering of Leucine Dehydrogenase for L-2-Aminobutyric Acid Production
Xu, J., Cheng, F., Fu, F.-T., et al. (2016) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-016-2369-0 · Cited by 24
A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery
Moine-Franel, A., Mareuil, F., Nilges, M., Ciambur, C. B., & Spérandio, O. (2024) · Scientific Data · doi:10.1038/s41597-024-03233-z · Cited by 25
Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations
Sampson, J. M., Cannon, D. A., Duan, J., Epstein, J. C. K., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S. M., Bahna, F. A., Adihou, H., Guéret, S. M., et al. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168640 · Cited by 24
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures
(2024) · doi:10.1038/s41592-024-02409-0 · Cited by 29
In Silico Prediction of the Effects of Mutations in the Human Mevalonate Kinase Gene: Towards a Predictive Framework for Mevalonate Kinase Deficiency
Browne, C., & Timson, D. J. (2015) · Annals of Human Genetics · doi:10.1111/ahg.12126 · Cited by 23
Protein Engineering of the Antitumor Enzyme PpADI for Improved Thermal Resistance
Zhu, L., Cheng, F., Piatkowski, V., & Schwaneberg, U. (2013) · ChemBioChem · doi:10.1002/cbic.201300433 · Cited by 23
Pathogenic mutations in retinitis pigmentosa 2 predominantly result in loss of RP2 protein stability in humans and zebrafish
Liu, F., Qin, Y., Yu, S., Soares, D. C., Yang, L., Weng, J., Li, C., Gao, M., Lu, Z., Hu, X., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.760314 · Cited by 23
De novo non-synonymous TBL1XR1 mutation alters Wnt signaling activity
Nishi, A., Numata, S., Tajima, A., Zhu, X., Ito, K., Saito, A., Kato, Y., Kinoshita, M., Shimodera, S., Ono, S., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-02792-z · Cited by 23
Population-specific design of de-immunized protein biotherapeutics
Schubert, B., Schärfe, C., Dönnes, P., Hopf, T. A., Marks, D. S., & Kohlbacher, O. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005983 · Cited by 24
The Gαi-GIV binding interface is a druggable protein-protein interaction
DiGiacomo, V., de Opakua, A. I., Papakonstantinou, M. P., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-08829-7 · Cited by 23
Functional Role and Hierarchy of the Intermolecular Interactions in Binding of Protein Kinase Clients to the Hsp90–Cdc37 Chaperone: Structure-Based Network Modeling of Allosteric Regulation
Stetz, G., & Verkhivker, G. M. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00638 · Cited by 23
Genetic polymorphism of Plasmodium falciparum circumsporozoite protein on Bioko Island, Equatorial Guinea and global comparative analysis
Huang, H., Liang, X., Lin, L., et al. (2020) · Malaria Journal · doi:10.1186/s12936-020-03315-4 · Cited by 23
StAmP-DB: a platform for structures of polymorphic amyloid fibril cores
Louros, N. N., van der Kant, R., Schymkowitz, J. W. H., & Rousseau, F. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac126 · Cited by 23
Self-citation
Structure-based dual affinity optimization of a SARS-CoV-1/2 cross-reactive single-domain antibody
Sulea, T. I., Baardsnes, J., Stuible, M., Rohani, N., Tran, A., Parat, M., Donates, Y. C., Duchesne, M., Plante, P., Kour, G., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0266250 · Cited by 23
Disulfide Bond Engineering for Enhancing the Thermostability of the Maltotetraose-Forming Amylase from Pseudomonas saccharophila STB07
Wang, Y., Li, C., Ban, X., et al. (2022) · Foods · doi:10.3390/foods11091207 · Cited by 23
Celastrol: A lead compound that inhibits SARS‐CoV‐2 replication, the activity of viral and human cysteine proteases, and virus‐induced IL‐6 secretion
Fuzo, C. A., Júnior, R. B. M., Fraga‐Silva, T. F. D. C., Amstalden, M. K., Léo, T. C. D., Souza, J. D. P., de Lima, T. M., Faccioli, L. H., Okamoto, D. N., Juliano, M. A., et al. (2022) · Drug Development Research · doi:10.1002/ddr.21982 · Cited by 22
A gain-of-function HCN4 mutant in the HCN domain is responsible for inappropriate sinus tachycardia in a Spanish family
Cámara‐Checa, A., Perín, F., Rubio‐Alarcón, M., Dago, M., Crespo‐García, T., Rapún, J., Marín, M., Cebrián, J., Gómez, R. J., Bermúdez-Jiménez, F. J., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2305135120 · Cited by 22
Identification and Glycerol-Induced Correction of Misfolding Mutations in the X-Linked Mental Retardation Gene CASK
LaConte, L. E. W., Chavan, V., & Mukherjee, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088276 · Cited by 23
Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by atomistic simulations and biophysical methods
Papaleo, E., Parravicini, F., Grandori, R., et al. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2014.09.018 · Cited by 23
Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses
Toufighi, K., Yang, J., Luis, N. M., Benitah, S. A., Lehner, B., Serrano, L. G., & Kiel, C. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004256 · Cited by 23
Self-citation
In silico analysis of nonsynonymous single nucleotide polymorphisms of the human adiponectin receptor 2 ( ADIPOR2 ) gene
Solayman, M., Saleh, M. A., Paul, S., et al. (2017) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2017.03.005 · Cited by 23
An Approach for a Synthetic CTL Vaccine Design against Zika Flavivirus Using Class I and Class II Epitopes Identified by Computer Modeling
Cunha‐Neto, E., Rosa, D. S., Harris, P. E., Olson, T., Morrow, A. M., Ciotlos, S., Herst, C. V., & Rubsamen, R. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00640 · Cited by 22
Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems
Barradas‐Bautista, D., Rosell, M., Pallara, C., & Fernández‐Recio, J. (2017) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2017.06.003 · Cited by 24
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy
Limviphuvadh, V., Tan, C., Konishi, F., et al. (2018) · BMC Cancer · doi:10.1186/s12885-018-4471-x · Cited by 23
Expanding the watch list for potential Ebola virus antibody escape mutations
Patel, J. S., Quates, C. J., Johnson, E. L., & Ytreberg, F. M. (2019) · PLoS ONE · doi:10.1371/journal.pone.0211093 · Cited by 23
The natural history of infantile mitochondrial DNA depletion syndrome due to RRM2B deficiency
Keshavan, N., Abdenur, J. E., Anderson, G. W., et al. (2019) · Genetics in Medicine · doi:10.1038/s41436-019-0613-z · Cited by 23
Estimating the Effect of Single-Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein
Banerjee, A., & Mitra, P. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00256 · Cited by 21
KnowVolution Campaign of an Aryl Sulfotransferase Increases Activity toward Cellobiose
Islam, S., Laaf, D., Infanzón, B., et al. (2018) · Chemistry - A European Journal · doi:10.1002/chem.201803729 · Cited by 23
Computer-Aided Reconstruction and Application of Bacillus halodurans S7 Xylanase with Heat and Alkali Resistance
Zhou, H., Cai, Y., Long, M., Zheng, N., Zhang, Z., You, C., Hussain, A., & Xia, X. (2024) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c08221 · Cited by 23
Structural and thermodynamic classification of amyloid polymorphs
Connor, J. P., Radford, S. E., & Brockwell, D. J. (2025) · Structure · doi:10.1016/j.str.2025.07.005 · Cited by 22
Specific Interaction between eEF1A and HIV RT Is Critical for HIV-1 Reverse Transcription and a Potential Anti-HIV Target
Li, D., Wei, T., Rawle, D. J., Fangyun, Q., Wang, R., Soares, D. C., Jin, H., Sivakumaran, H., Lin, M., Spann, K. M., et al. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005289 · Cited by 23
Stability Effects of Protein Mutations: The Role of Long-Range Contacts
Bigman, L. S., & Levy, Y. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b07379 · Cited by 22
A first continuous 4-aminoantipyrine (4-AAP)-based screening system for directed esterase evolution
Lülsdorf, N., Vojcic, L., Hellmuth, H., Weber, T. T., Mußmann, N., Martínez, R., & Schwaneberg, U. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6612-3 · Cited by 22
Damaging coding variants within kainate receptor channel genes are enriched in individuals with schizophrenia, autism and intellectual disabilities
Koromina, M., Flitton, M., Blockley, A., Mellor, I. R., & Knight, H. M. (2019) · Scientific Reports · doi:10.1038/s41598-019-55635-4 · Cited by 22
DiRect: Site-directed mutagenesis method for protein engineering by rational design
Watanabe, S., Ito, M., & Kigawa, T. (2021) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2021.03.021 · Cited by 23
Computational decomposition reveals reshaping of the SARS‐CoV‐2–ACE2 interface among viral variants expressing the N501Y mutation
Socher, E., Conrad, M., Heger, L., Paulsen, F. P., Sticht, H., Zunke, F., & Arnold, P. (2021) · Journal of Cellular Biochemistry · doi:10.1002/jcb.30142 · Cited by 22
Differential regulation of insulin signalling by monomeric and oligomeric amyloid beta-peptide
Molina-Fernández, R., Picón-Pagès, P., Barranco-Almohalla, A., Crepin, G., Herrera-Fernández, V., García-Elías, A., Fanlo-Ucar, H., Fernàndez‐Busquets, X., García‐Ojalvo, J., Oliva, B., et al. (2022) · Brain Communications · doi:10.1093/braincomms/fcac243 · Cited by 23
Challenges in predicting stabilizing variations: An exploration
Benevenuta, S., Birolo, G., Sanavia, T., Capriotti, E., & Fariselli, P. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1075570 · Cited by 23
Glycan masking of a non-neutralising epitope enhances neutralising antibodies targeting the RBD of SARS-CoV-2 and its variants
Carnell, G., Billmeier, M., Vishwanath, S., Sans, M. S., Wein, H., George, C. L., Neckermann, P., Rosario, J. M. M. D., Sampson, A., Einhauser, S., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1118523 · Cited by 21
PRA-Pred: Structure-based prediction of protein-RNA binding affinity
Harini, K., Sekijima, M., & Gromiha, M. M. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.129490 · Cited by 22
Structural Model for the Interaction of a Designed Ankyrin Repeat Protein with the Human Epidermal Growth Factor Receptor 2
Epa, V. C., Dolezal, O., Doughty, L., Xiao, X., Jöst, C., Plückthun, A., & Adams, T. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059163 · Cited by 22
Binding of flavonoids to staphylococcal enterotoxin B
Benedik, E., Skrt, M., Podlipnik, Č., et al. (2014) · Food and Chemical Toxicology · doi:10.1016/j.fct.2014.08.012 · Cited by 22
In Silico Screening, Genotyping, Molecular Dynamics Simulation and Activity Studies of SNPs in Pyruvate Kinase M2
Ponnusamy, K., Kumar, B., Chopra, R., Gupta, V., Subbarao, N., & Bamezai, R. N. K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0120469 · Cited by 22
Functional Null Mutations in the Gonosomal Homologue Gene TBL1Y are Associated with Non-Syndromic Coarctation of the Aorta
Tagariello, A., Breuer, C., Birkner, Y., Schmidt, S., Koch, A., Cesnjevar, R. A., Rüffer, A., Dittrich, S., Schneider, H., Winterpacht, A., et al. (2012) · Current Molecular Medicine · doi:10.2174/156652412798889027 · Cited by 22
Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes
Gress, A., Ramensky, V. E., & Kalinina, O. V. (2017) · Oncogenesis · doi:10.1038/oncsis.2017.79 · Cited by 22
Structural effects of point mutations in proteins
Shanthirabalan, S., Chomilier, J., & Carpentier, M. (2018) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25499 · Cited by 24
Biallelic variants in DNA2 cause microcephalic primordial dwarfism
Tarnauskaitė, Ž., Bicknell, L. S., Marsh, J. A., Murray, J., Parry, D. A., Logan, C. V., Bober, M. B., de Silva, D. C., Duker, A. L., Sillence, D. O., et al. (2019) · Human Mutation · doi:10.1002/humu.23776 · Cited by 21
Revisiting silibinin as a novobiocin-like Hsp90 C-terminal inhibitor: Computational modeling and experimental validation
Cuyàs, E., Verdura, S., Micol, V., Joven, J., Bosch‐Barrera, J., Encinar, J. A., & Menéndez, J. A. (2019) · Food and Chemical Toxicology · doi:10.1016/j.fct.2019.110645 · Cited by 23
Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction
Potthoff, J., Bojarski, K. K., Kohut, G., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20205021 · Cited by 22
Species-Specific Evolution of Ebola Virus during Replication in Human and Bat Cells
Whitfield, Z. J., Prasad, A. N., Ronk, A. J., Kuzmin, I. V., Ilinykh, P. A., Andino, R., & Bukreyev, A. A. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108028 · Cited by 27
Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions
Meseguer, A., Dominguez, L., Bota, P. M., Aguirre‐Plans, J., Bonet, J., Fernández‐Fuentes, N., & Oliva, B. (2020) · Protein Science · doi:10.1002/pro.3930 · Cited by 21
Similar but Not Identical—Binding Properties of LSU (Response to Low Sulfur) Proteins From Arabidopsis thaliana
Niemiro, A., Cysewski, D., Brzywczy, J., et al. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.01246 · Cited by 22
Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputingPreprint
Desautels, T., Zemla, A. T., Lau, E. Y., Franco, M., & Faissol, D. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.03.024885 · Cited by 21
Simple computational methods can outperform deep learning in designing diverse, binder-enriched antibody librariesPreprint
Chinery, L., Hummer, A. M., Mehta, B. B., Akbar, R., Rawat, P., Slabodkin, A., Quý, K. L., Lund‐Johansen, F., Greiff, V., Jeliazkov, J. R., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.26.586756 · Cited by 22
AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactionsPreprint
Lu, W., Zhang, J., Rao, J., Zhang, Z., & Zheng, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.25.595871 · Cited by 27
Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study
(2024) · doi:10.1128/msphere.00799-23 · Cited by 23
Understanding the heterogeneous performance of variant effect predictors across human protein-coding genes
Fawzy, M., & Marsh, J. A. (2024) · Scientific Reports · doi:10.1038/s41598-024-76202-6 · Cited by 22
Computational structural optimization enhances IL13Rα2 – B7-H3 tandem CAR T cells to overcome antigen-heterogeneity-mediated tumor escape
Meehl, M. M., Immadisetty, K., Trivedi, V. D., Głowacki, P., Prinzing, B. L., Anido, A. A., Ibañez-Vega, J., Leslie, B. J., Babu, M. M., & Krenciute, G. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.07.044 · Cited by 21
Loop engineering in enzymes from structure to function: Mechanisms, methodologies, and engineering strategies
Song, C., Gu, J., Ren, H., Li, Z., Xie, D., Han, L., Qiao, J., Cheng, Z., Nie, Y., & Zhou, Z. (2025) · Biotechnology Advances · doi:10.1016/j.biotechadv.2025.108716 · Cited by 21
Generalizable and scalable protein stability prediction with rewired protein generative models
Li, Z., & Luo, Y. (2025) · Nature Communications · doi:10.1038/s41467-025-67609-4 · Cited by 24
How to engineer glucose oxidase for mediated electron transfer
Gutierrez, E. A., Wallraf, A., Balaceanu, A., Bocola, M., Davari, M. D., Meier, T., Duefel, H., & Schwaneberg, U. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26785 · Cited by 21
Contributions of Net Charge on the PlyC Endolysin CHAP Domain
Shang, X., & Nelson, D. C. (2019) · Antibiotics · doi:10.3390/antibiotics8020070 · Cited by 21
Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1
Caswell, R. C., Owens, M., Gunning, A. C., et al. (2019) · Journal of the Endocrine Society · doi:10.1210/js.2019-00260 · Cited by 21
Parallel Strategy Increases the Thermostability and Activity of Glutamate Decarboxylase
Zhang, Q.-F., Hu, S. C., Zhao, W., et al. (2020) · Molecules · doi:10.3390/molecules25030690 · Cited by 21
Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism
Kumar, S. P., Patel, C., Rawal, R., & Pandya, H. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25894 · Cited by 21
Bacteria use structural imperfect mimicry to hijack the host interactome
de Groot, N. S., & Torrent, M. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008395 · Cited by 21
Assessment of software methods for estimating protein-protein relative binding affinities
Gonzalez, T. R., Martin, K., Barnes, J. E., Patel, J. S., & Ytreberg, F. M. (2020) · PLoS ONE · doi:10.1371/journal.pone.0240573 · Cited by 22
Globally defining the effects of mutations in a picornavirus capsid
Mattenberger, F., Latorre, V., Tirosh, O., Stern, A., & Geller, R. (2021) · eLife · doi:10.7554/elife.64256 · Cited by 24
Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Šoštarić, N., & van Noort, V. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008988 · Cited by 23
Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance
Mugumbate, G., Nyathi, B., Zindoga, A., et al. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.643849 · Cited by 21
Improved thermostability of proteinase K and recognizing the synergistic effect of Rosetta and FoldX approaches
Zhao, Y., Li, D., Bai, X., et al. (2021) · Protein Engineering Design and Selection · doi:10.1093/protein/gzab024 · Cited by 21
Heterotypic amyloid interactions: Clues to polymorphic bias and selective cellular vulnerability?
Louros, N. N., Schymkowitz, J. W. H., & Rousseau, F. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.11.007 · Cited by 19
Self-citation
Current and Emerging Tools of Computational Biology To Improve the Detoxification of Mycotoxins
Sandlin, N., Kish, D. R., Kim, J., Zaccaria, M., & Momeni, B. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.02102-21 · Cited by 21
pyFoldX: enabling biomolecular analysis and engineering along structural ensembles
Radusky, L., & Serrano, L. G. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac072 · Cited by 19
Self-citation
Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome
Cousin, M. A., Veale, E. L., Dsouza, N. R., Tripathi, S., Holden, R. G., Arélin, M., Beek, G. J., Bekheirnia, M. R., Beygo, J., Bhambhani, V., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01064-4 · Cited by 21
A limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures
Toll‐Riera, M., Olombrada, M., Castro-Giner, F., & Wagner, A. (2022) · Science Advances · doi:10.1126/sciadv.abk3511 · Cited by 19
Protein engineering for feedback resistance in 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
Jayaraman, K., Trachtmann, N. V., Sprenger, G. A., & Gohlke, H. (2022) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-022-12166-9 · Cited by 21
Structure and Dynamics of the Unassembled Nucleoprotein of Rabies Virus in Complex with Its Phosphoprotein Chaperone Module
Gérard, F. C. A., Bourhis, J., Mas, C., Branchard, A., Vu, D., Varhoshkova, S., Leyrat, C., & Jamin, M. (2022) · Viruses · doi:10.3390/v14122813 · Cited by 21
SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19
Temmam, S., Montagutelli, X., Hérate, C., Donati, F., Regnault, B., Attia, M., Baquero, E., Chrétien, D., Conquet, L., Jouvion, G., et al. (2023) · EMBO Reports · doi:10.15252/embr.202256055 · Cited by 24
Two single-point mutations in Ankyrin Repeat one drastically change the threshold temperature of TRPV1
Hori, S., Tateyama, M., Shirai, T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38051-1 · Cited by 21
Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling
Sankhe, G. D., Raja, R., Singh, D. P., Bheemireddy, S., Rana, S., Athira, P. J., Dixit, N. M., & Saini, D. K. (2023) · Nature Communications · doi:10.1038/s41467-023-40095-2 · Cited by 23
Improving the thermal stability and catalytic activity of ulvan lyase by the combination of FoldX and KnowVolution campaign
Huang, A., Chen, Z., Wu, X., et al. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.128577 · Cited by 21
Fragment-based drug discovery and protein–protein interactions
Turnbull, A. P., Boyd, S., & Walse, B. (2014) · Research and Reports in Biochemistry · doi:10.2147/rrbc.s28428 · Cited by 21
Crucial Roles of Single Residues in Binding Affinity, Specificity, and Promiscuity in the Cellulosomal Cohesin-Dockerin Interface
Slutzki, M., Reshef, D., Barak, Y., Haimovitz, R., Rotem‐Bamberger, S., Lamed, R., Bayer, E. A., & Schueler‐Furman, O. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.651208 · Cited by 21

Authors: Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L.
Affiliations: Vrije Universiteit Brussel (BE)
University of Copenhagen (DK)
European Molecular Biology Laboratory (DE)
Corresponding author: Schymkowitz, J.
ORCID: Schymkowitz, J.
Stricher, F.
Nys, R.
Rousseau, F.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2005-07-01
Volume: 33
Issue: Web Server
Pages: W382-W388
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gki387
PMC: PMC1160148
OpenAlex: W2023490488
Semantic Scholar: 18ceb01ed1614dfc42404e0e2d838443cc0a4731
Cited by: 2,759
References: 23
Citations by year: 2026: 222 · 2025: 298 · 2024: 254 · 2023: 264 · 2022: 215 · 2021: 227 · 2020: 223 · 2019: 181 · 2018: 150 · 2017: 113 · 2016: 99 · 2015: 96 · 2014: 90 · 2013: 65 · 2012: 65
FWCI: 9.29
Type: journal article
Language: en
Open access: gold
doi.org
Licence: public-domain
Locations: Nucleic Acids Research (publishedVersion, public-domain)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
VUBIR (Vrije Universiteit Brussel) (submittedVersion)
Funders: European Commission
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: FoldX, empirical force fields, protein stability, free energy calculation, protein folding, protein dynamics, nucleic acids, mutation effects, proton positions, water bridges, metal binding sites, complex formation, alanine scanning
MeSH terms: Mutation, Nucleic Acid Conformation, Protein Conformation, Proteins, Software, Molecular Structure, Protein Folding, Internet, Polymorphism, Single Nucleotide, Databases, Protein

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The FoldX web server: an online force field

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks