mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance
暂无分享,去创建一个
[1] Douglas E. V. Pires,et al. Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. , 2015, JIMD reports.
[2] Douglas E. V. Pires,et al. mCSM: predicting the effects of mutations in proteins using graph-based signatures , 2013, Bioinform..
[3] David T. W. Jones,et al. Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions , 2014, Nucleic acids research.
[4] François Stricher,et al. The FoldX web server: an online force field , 2005, Nucleic Acids Res..
[5] Douglas E. V. Pires,et al. CSM-lig: a web server for assessing and comparing protein–small molecule affinities , 2016, Nucleic Acids Res..
[6] A. Skerra,et al. Small antibody-like proteins with prescribed ligand specificities derived from the lipocalin fold. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[7] K. Anderson,et al. Current Perspectives on HIV-1 Antiretroviral Drug Resistance , 2014, Viruses.
[8] J. Mccammon,et al. HIV‐1 protease molecular dynamics of a wild‐type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs , 2004, Protein science : a publication of the Protein Society.
[9] Douglas E. V. Pires,et al. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach , 2014, Nucleic Acids Res..
[10] Jerome Wielens,et al. Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA , 2014, Scientific Reports.
[11] E. Arnold,et al. Multifaceted Roles of Crystallography in Modern Drug Discovery , 2015, NATO Science for Peace and Security Series A: Chemistry and Biology.
[12] Douglas E. V. Pires,et al. Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes , 2014, Nucleic Acids Res..
[13] R. Cherny,et al. Regulation of insulin-regulated membrane aminopeptidase activity by its C-terminal domain. , 2011, Biochemistry.
[14] Akinori Sarai,et al. ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions , 2005, Nucleic Acids Res..
[15] Douglas E. V. Pires,et al. pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures , 2015, Journal of medicinal chemistry.
[16] Michael W Parker,et al. Identification and characterization of a new cognitive enhancer based on inhibition of insulin‐regulated aminopeptidase , 2008, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[17] Simona Soverini,et al. BCR-ABL kinase domain mutation analysis in chronic myeloid leukemia patients treated with tyrosine kinase inhibitors: recommendations from an expert panel on behalf of European LeukemiaNet. , 2011, Blood.
[18] T L Blundell,et al. Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. , 1997, Protein engineering.
[19] Michael W Parker,et al. Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase. , 2008, Biochemistry and cell biology = Biochimie et biologie cellulaire.
[20] Michael W Parker,et al. Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase , 2008, BMC Neuroscience.
[21] D. Gibbons,et al. Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy , 2014, Proceedings of the National Academy of Sciences.
[22] Douglas E. V. Pires,et al. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance , 2016, BMC Medicine.
[23] P. Shannon,et al. Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.
[24] Douglas E. V. Pires,et al. mCSM-AB: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures , 2016, Nucleic Acids Res..
[25] Douglas E. V. Pires,et al. Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma. , 2015, Cancer discovery.
[26] Wagner Meira,et al. PDBest: a user-friendly platform for manipulating and enhancing protein structures , 2015, Bioinform..
[27] Christopher K. I. Williams,et al. Gaussian Processes for Machine Learning (Adaptive Computation and Machine Learning) , 2005 .
[28] Wagner Meira,et al. Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns , 2011, BMC Genomics.
[29] F. Baquero,et al. Tackling antibiotic resistance: the environmental framework , 2015, Nature Reviews Microbiology.
[30] Mallur S. Madhusudhan,et al. Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins , 2013, Nucleic Acids Res..
[31] R. Lamb,et al. Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. , 2011, Journal of the American Chemical Society.
[32] Kenny Q. Ye,et al. An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.
[33] Douglas E. V. Pires,et al. In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity , 2016, Scientific Reports.
[34] Juan Fernández-Recio,et al. SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models , 2012, Bioinform..
[35] Rational engineering of a fluorescein-binding anticalin for improved ligand affinity , 2005, Biological chemistry.
[36] Guy Boivin,et al. Impact of Neuraminidase Mutations Conferring Influenza Resistance to Neuraminidase Inhibitors in the N1 and N2 Genetic Backgrounds , 2006, Antiviral therapy.
[37] Tom L. Blundell,et al. Flexibility and small pockets at protein–protein interfaces: New insights into druggability , 2015, Progress in biophysics and molecular biology.
[38] Piero Fariselli,et al. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure , 2005, Nucleic Acids Res..
[39] Marianne Rooman,et al. BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations , 2013, Nucleic Acids Res..
[40] Ludevit Kadasi,et al. Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on ‘black bone disease’ in Italy , 2015, European Journal of Human Genetics.
[41] Philippe Bogaerts,et al. Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 , 2009, Bioinform..