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For: Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics 2008;24:i207-12. [PMID: 18689826 PMCID: PMC2597370 DOI: 10.1093/bioinformatics/btn268] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Sardag I, Duvenci ZS, Belkaya S, Timucin E. Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers. Comput Struct Biotechnol J 2024;23:1854-1863. [PMID: 38882680 PMCID: PMC11177541 DOI: 10.1016/j.csbj.2024.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 06/18/2024]  Open
2
Vorontsov IE, Kozin I, Abramov S, Boytsov A, Jolma A, Albu M, Ambrosini G, Faltejskova K, Gralak AJ, Gryzunov N, Inukai S, Kolmykov S, Kravchenko P, Kribelbauer-Swietek JF, Laverty KU, Nozdrin V, Patel ZM, Penzar D, Plescher ML, Pour SE, Razavi R, Yang AWH, Yevshin I, Zinkevich A, Weirauch MT, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Kolpakov FA, Makeev VJ, Hughes TR, Kulakovskiy IV. Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.11.619379. [PMID: 39605530 PMCID: PMC11601219 DOI: 10.1101/2024.11.11.619379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
3
O’Brien BCV, Thao S, Weber L, Danielson HL, Boldt AD, Hueffer K, Weltzin MM. The human alpha7 nicotinic acetylcholine receptor is a host target for the rabies virus glycoprotein. Front Cell Infect Microbiol 2024;14:1394713. [PMID: 38836054 PMCID: PMC11148329 DOI: 10.3389/fcimb.2024.1394713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/29/2024] [Indexed: 06/06/2024]  Open
4
Wenzel M, Grüner E, Strodthoff N. Insights into the inner workings of transformer models for protein function prediction. Bioinformatics 2024;40:btae031. [PMID: 38244570 PMCID: PMC10950482 DOI: 10.1093/bioinformatics/btae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024]  Open
5
Hall MWJ, Shorthouse D, Alcraft R, Jones PH, Hall BA. Mutations observed in somatic evolution reveal underlying gene mechanisms. Commun Biol 2023;6:753. [PMID: 37468606 PMCID: PMC10356810 DOI: 10.1038/s42003-023-05136-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]  Open
6
Marquet C, Heinzinger M, Olenyi T, Dallago C, Erckert K, Bernhofer M, Nechaev D, Rost B. Embeddings from protein language models predict conservation and variant effects. Hum Genet 2022;141:1629-1647. [PMID: 34967936 PMCID: PMC8716573 DOI: 10.1007/s00439-021-02411-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
7
Comprehensive mutagenesis identifies the peptide repertoire of a p53 T-cell receptor mimic antibody that displays no toxicity in mice transgenic for human HLA-A*0201. PLoS One 2021;16:e0249967. [PMID: 33836029 PMCID: PMC8034716 DOI: 10.1371/journal.pone.0249967] [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: 12/28/2020] [Accepted: 03/11/2021] [Indexed: 11/24/2022]  Open
8
Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, Montgomery SB, Chang HY, Montine TJ. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet 2020;52:1158-1168. [PMID: 33106633 PMCID: PMC7606627 DOI: 10.1038/s41588-020-00721-x] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
9
Qiu J, Nechaev D, Rost B. Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human. BMC Bioinformatics 2020;21:452. [PMID: 33050876 PMCID: PMC7557062 DOI: 10.1186/s12859-020-03759-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/16/2020] [Indexed: 11/10/2022]  Open
10
Shrikumar A, Prakash E, Kundaje A. GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs. Bioinformatics 2020;35:i173-i182. [PMID: 31510661 PMCID: PMC6612808 DOI: 10.1093/bioinformatics/btz322] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
11
Wada M, Hayashi Y, Arai M. Mutational analysis of a catalytically important loop containing active site and substrate-binding site in Escherichia coli phytase AppA. Biosci Biotechnol Biochem 2019;83:860-868. [DOI: 10.1080/09168451.2019.1571897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
12
Raimondi D, Orlando G, Tabaro F, Lenaerts T, Rooman M, Moreau Y, Vranken WF. Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome. Sci Rep 2018;8:16980. [PMID: 30451933 PMCID: PMC6242909 DOI: 10.1038/s41598-018-34959-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022]  Open
13
Roxas JL, Monasky RC, Roxas BAP, Agellon AB, Mansoor A, Kaper JB, Vedantam G, Viswanathan V. Enteropathogenic Escherichia coli EspH-Mediated Rho GTPase Inhibition Results in Desmosomal Perturbations. Cell Mol Gastroenterol Hepatol 2018;6:163-180. [PMID: 30003123 PMCID: PMC6039986 DOI: 10.1016/j.jcmgh.2018.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 04/20/2018] [Indexed: 12/27/2022]
14
Pandey B, Grover S, Goyal S, Kumari A, Singh A, Jamal S, Kaur J, Grover A. Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region. Sci Rep 2018;8:903. [PMID: 29343701 PMCID: PMC5772511 DOI: 10.1038/s41598-017-19075-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/19/2017] [Indexed: 02/01/2023]  Open
15
Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions. Genetics 2017;207:53-61. [PMID: 28751422 PMCID: PMC5586385 DOI: 10.1534/genetics.117.300064] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 07/24/2017] [Indexed: 11/18/2022]  Open
16
Edrees BM, Athar M, Abduljaleel Z, Al-Allaf FA, Taher MM, Khan W, Bouazzaoui A, Al-Harbi N, Safar R, Al-Edressi H, Alansary K, Anazi A, Altayeb N, Ahmed MA. Functional alterations due to amino acid changes and evolutionary comparative analysis of ARPKD and ADPKD genes. GENOMICS DATA 2016;10:127-134. [PMID: 27843768 PMCID: PMC5099264 DOI: 10.1016/j.gdata.2016.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/18/2016] [Accepted: 10/30/2016] [Indexed: 12/15/2022]
17
Reeb J, Hecht M, Mahlich Y, Bromberg Y, Rost B. Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLoS Comput Biol 2016;12:e1005047. [PMID: 27536940 PMCID: PMC4990455 DOI: 10.1371/journal.pcbi.1005047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/04/2016] [Indexed: 11/19/2022]  Open
18
Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, Costa J, Bonvin AMJJ, Moreira IS. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Int J Mol Sci 2016;17:E1215. [PMID: 27472327 PMCID: PMC5000613 DOI: 10.3390/ijms17081215] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022]  Open
19
Al-Allaf FA, Alashwal A, Abduljaleel Z, Taher MM, Siddiqui SS, Bouazzaoui A, Abalkhail H, Aun R, Al-Allaf AF, AbuMansour I, Azhar Z, Ba-Hammam FA, Khan W, Athar M. Identification of a recurrent frameshift mutation at the LDLR exon 14 (c.2027delG, p.(G676Afs*33)) causing familial hypercholesterolemia in Saudi Arab homozygous children. Genomics 2015;107:24-32. [PMID: 26688439 DOI: 10.1016/j.ygeno.2015.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/06/2015] [Accepted: 12/09/2015] [Indexed: 11/25/2022]
20
Hecht M, Bromberg Y, Rost B. Better prediction of functional effects for sequence variants. BMC Genomics 2015;16 Suppl 8:S1. [PMID: 26110438 PMCID: PMC4480835 DOI: 10.1186/1471-2164-16-s8-s1] [Citation(s) in RCA: 403] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
21
Flores DI, Sotelo-Mundo RR, Brizuela CA. A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations. PLoS One 2014;9:e108513. [PMID: 25268770 PMCID: PMC4182483 DOI: 10.1371/journal.pone.0108513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/31/2014] [Indexed: 11/23/2022]  Open
22
Anand P, Nagarajan D, Mukherjee S, Chandra N. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. F1000Res 2014;3:214. [PMID: 25685322 DOI: 10.12688/f1000research.5165.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2014] [Indexed: 03/24/2024]  Open
23
Anand P, Nagarajan D, Mukherjee S, Chandra N. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. F1000Res 2014;3:214. [PMID: 25685322 PMCID: PMC4319546 DOI: 10.12688/f1000research.5165.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/24/2014] [Indexed: 12/27/2022]  Open
24
Abduljaleel Z, Al-Allaf FA, Khan W, Athar M, Shahzad N, Taher MM, Elrobh M, Alanazi MS, El-Huneidi W. Evidence of trem2 variant associated with triple risk of Alzheimer's disease. PLoS One 2014;9:e92648. [PMID: 24663666 PMCID: PMC3963925 DOI: 10.1371/journal.pone.0092648] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 02/25/2014] [Indexed: 12/27/2022]  Open
25
Ozbek P, Soner S, Haliloglu T. Hot spots in a network of functional sites. PLoS One 2013;8:e74320. [PMID: 24023934 PMCID: PMC3759471 DOI: 10.1371/journal.pone.0074320] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 08/02/2013] [Indexed: 12/05/2022]  Open
26
Weinzierl ROJ. The RNA polymerase factory and archaeal transcription. Chem Rev 2013;113:8350-76. [PMID: 23978070 DOI: 10.1021/cr400148k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
27
Hecht M, Bromberg Y, Rost B. News from the protein mutability landscape. J Mol Biol 2013;425:3937-48. [PMID: 23896297 DOI: 10.1016/j.jmb.2013.07.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/08/2013] [Accepted: 07/19/2013] [Indexed: 12/16/2022]
28
Dehouck Y, Kwasigroch JM, Rooman M, Gilis D. BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations. Nucleic Acids Res 2013;41:W333-9. [PMID: 23723246 PMCID: PMC3692068 DOI: 10.1093/nar/gkt450] [Citation(s) in RCA: 268] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
29
Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics 2012;13 Suppl 4:S11. [PMID: 22759649 PMCID: PMC3394413 DOI: 10.1186/1471-2164-13-s4-s11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
30
Gray VE, Kukurba KR, Kumar S. Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. Bioinformatics 2012;28:2093-6. [PMID: 22685075 PMCID: PMC3413386 DOI: 10.1093/bioinformatics/bts336] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
31
Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2). Mol Divers 2012;16:401-13. [PMID: 22528270 DOI: 10.1007/s11030-012-9368-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 03/16/2012] [Indexed: 10/28/2022]
32
Koes DR, Camacho CJ. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res 2012;40:W387-92. [PMID: 22523085 PMCID: PMC3394328 DOI: 10.1093/nar/gks336] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
33
Adams DR, Sincan M, Fuentes Fajardo K, Mullikin JC, Pierson TM, Toro C, Boerkoel CF, Tifft CJ, Gahl WA, Markello TC. Analysis of DNA sequence variants detected by high-throughput sequencing. Hum Mutat 2012;33:599-608. [PMID: 22290882 DOI: 10.1002/humu.22035] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/02/2011] [Indexed: 12/18/2022]
34
Koes DR, Camacho CJ. Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. ACTA ACUST UNITED AC 2011;28:784-91. [PMID: 22210869 PMCID: PMC3307105 DOI: 10.1093/bioinformatics/btr717] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
35
Mencarelli M, Dubern B, Alili R, Maestrini S, Benajiba L, Tagliaferri M, Galan P, Rinaldi M, Simon C, Tounian P, Hercberg S, Liuzzi A, Di Blasio AM, Clement K. Rare melanocortin-3 receptor mutations with in vitro functional consequences are associated with human obesity. Hum Mol Genet 2010;20:392-9. [PMID: 21047972 DOI: 10.1093/hmg/ddq472] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
36
Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE. Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics 2010;11:242. [PMID: 20459833 PMCID: PMC2885373 DOI: 10.1186/1471-2105-11-242] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 05/11/2010] [Indexed: 12/02/2022]  Open
37
Izarzugaza JMG, Redfern OC, Orengo CA, Valencia A. Cancer-associated mutations are preferentially distributed in protein kinase functional sites. Proteins 2010;77:892-903. [PMID: 19626714 DOI: 10.1002/prot.22512] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
38
Lise S, Archambeau C, Pontil M, Jones DT. Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics 2009;10:365. [PMID: 19878545 PMCID: PMC2777894 DOI: 10.1186/1471-2105-10-365] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 10/30/2009] [Indexed: 11/10/2022]  Open
39
Bromberg Y, Overton J, Vaisse C, Leibel RL, Rost B. In silico mutagenesis: a case study of the melanocortin 4 receptor. FASEB J 2009;23:3059-69. [PMID: 19417090 PMCID: PMC2735358 DOI: 10.1096/fj.08-127530] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
40
Won HH, Kim JW. In Silico Functional Assessment of Sequence Variations: Predicting Phenotypic Functions of Novel Variations. Genomics Inform 2008. [DOI: 10.5808/gi.2008.6.4.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
41
Calton MA, Ersoy BA, Zhang S, Kane JP, Malloy MJ, Pullinger CR, Bromberg Y, Pennacchio LA, Dent R, McPherson R, Ahituv N, Vaisse C. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Hum Mol Genet 2008;18:1140-7. [PMID: 19091795 DOI: 10.1093/hmg/ddn431] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
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Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics 2008;24:2397-8. [PMID: 18757876 PMCID: PMC2562009 DOI: 10.1093/bioinformatics/btn435] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 08/10/2008] [Accepted: 08/14/2008] [Indexed: 11/13/2022]  Open
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