Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

Shoichet, 1995, A relationship between protein stability and protein function, Proc. Natl. Acad. Sci. USA, 92, 452, 10.1073/pnas.92.2.452

Pepys, 1993, Human lysozyme gene mutations cause hereditary systemic amyloidosis, Nature, 362, 553, 10.1038/362553a0

Hartley, 1993, Directed mutagenesis and barnase-barstar recognition, Biochemistry, 32, 5978, 10.1021/bi00074a008

Buckle, 1994, Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-A resolution, Biochemistry, 33, 8878, 10.1021/bi00196a004

Schreiber, 1995, Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles, J. Mol. Biol., 248, 478, 10.1016/S0022-2836(95)80064-6

Wang, 2004, How optimal are the binding energetics of barnase and barstar?, Biophys. J., 87, 1618, 10.1529/biophysj.104.040964

Spång, H.C.L., Braathen, R., and Bogen, B. (2012). Heterodimeric Barnase-Barstar Vaccine Molecules: Influence of One versus Two Targeting Units Specific for Antigen Presenting Cells. PLoS ONE, 7.

Richards, 1974, The interpretation of protein structures: Total volume, group volume distributions and packing density, J. Mol. Biol., 82, 1, 10.1016/0022-2836(74)90570-1

Dill, 1990, Dominant forces in protein folding, Biochemistry, 29, 7133, 10.1021/bi00483a001

Basu, S., Bhattacharyya, D., and Banerjee, R. (2011). Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs. BMC Bioinf., 12.

Javadpour, 1999, Helix packing in polytopic membrane proteins: Role of glycine in transmembrane helix association, Biophys. J., 77, 1609, 10.1016/S0006-3495(99)77009-8

Eilers, 2000, Internal packing of helical membrane proteins, Proc. Natl. Acad. Sci. USA, 97, 5796, 10.1073/pnas.97.11.5796

Banerjee, 2003, The jigsaw puzzle model: Search for conformational specificity in protein interiors, J. Mol. Biol., 333, 211, 10.1016/j.jmb.2003.08.013

Charneski, 2014, Positive charge loading at protein termini is due to membrane protein topology, not a translational ramp, Mol. Biol. Evol., 31, 70, 10.1093/molbev/mst169

Harley, 1996, The Role of Charged Residues in Determining Transmembrane Protein Insertion Orientation in Yeast, J. Biol. Chem., 271, 24625, 10.1074/jbc.271.40.24625

Uversky, 2013, Unusual biophysics of intrinsically disordered proteins, Biochim. Biophys. Acta, 1834, 932, 10.1016/j.bbapap.2012.12.008

Skach, 2009, Cellular mechanisms of membrane protein folding, Nat. Struct. Mol. Biol., 16, 606, 10.1038/nsmb.1600

Nakamura, 1996, Roles of electrostatic interaction in proteins, Q. Rev. Biophys., 29, 1, 10.1017/S0033583500005746

Basu, 2018, Salt-bridge dynamics in intrinsically disordered proteins: A trade-off between electrostatic interactions and structural flexibility, Biochim. Biophys. Acta (BBA) Proteins Proteom., 1866, 624, 10.1016/j.bbapap.2018.03.002

Coskuner-Weber, O., and Uversky, V.N. (2018). Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int. J. Mol. Sci., 19.

Gassner, 1996, A test of the “jigsaw puzzle” model for protein folding by multiple methionine substitutions within the core of T4 lysozyme, Proc. Natl. Acad. Sci. USA, 93, 12155, 10.1073/pnas.93.22.12155

Basu, 2014, Applications of complementarity plot in error detection and structure validation of proteins, Indian J. Biochem. Biophys., 51, 188

Liang, 2012, Computational studies of membrane proteins: Models and predictions for biological understanding, Biochim. Biophys. Acta (BBA) Biomembr., 1818, 927, 10.1016/j.bbamem.2011.09.026

Taylor, 2008, Mutations Affecting the Oligomerization Interface of G-Protein-Coupled Receptors Revealed by a Novel De Novo Protein Design Framework, Biophys. J., 94, 2470, 10.1529/biophysj.107.117622

Zhou, 2000, Building a Thermostable Membrane Protein, J. Biol. Chem., 275, 6975, 10.1074/jbc.275.10.6975

Schmidt, T., Situ, A.J., and Ulmer, T.S. (2016). Structural and thermodynamic basis of proline-induced transmembrane complex stabilization. Sci. Rep., 6.

Zhu, H., Sepulveda, E., Hartmann, M.D., Kogenaru, M., Ursinus, A., Sulz, E., Albrecht, R., Coles, M., Martin, J., and Lupas, A.N. (2016). Origin of a folded repeat protein from an intrinsically disordered ancestor. eLife, 5.

Baruah, 2016, Globular–disorder transition in proteins: A compromise between hydrophobic and electrostatic interactions?, Phys. Chem. Chem. Phys., 18, 23207, 10.1039/C6CP03185D

Huse, 2002, The conformational plasticity of protein kinases, Cell, 109, 275, 10.1016/S0092-8674(02)00741-9

Mas, G., and Hiller, S. (2018). Conformational plasticity of molecular chaperones involved in periplasmic and outer membrane protein folding. FEMS Microbiol. Lett., 365.

Ikura, 2006, Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: Two ways to promote multifunctionality, Proc. Natl. Acad. Sci. USA, 103, 1159, 10.1073/pnas.0508640103

Bastolla, 2013, The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly, Biochim. Biophys. Acta, 1834, 817, 10.1016/j.bbapap.2013.03.016

Buckle, 1996, Structural and energetic responses to cavity-creating mutations in hydrophobic cores: Observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities, Biochemistry, 35, 4298, 10.1021/bi9524676

Eriksson, 1992, Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect, Science, 255, 178, 10.1126/science.1553543

Axe, 1996, Active barnase variants with completely random hydrophobic cores, Proc. Natl. Acad. Sci. USA, 93, 5590, 10.1073/pnas.93.11.5590

Dahiyat, 1997, De novo protein design: Towards fully automated sequence selection, J. Mol. Biol., 273, 789, 10.1006/jmbi.1997.1341

Goraj, 1990, Synthesis, purification and initial structural characterization of octarellin, a de novo polypeptide modelled on the alpha/beta-barrel proteins, Protein Eng., 3, 259, 10.1093/protein/3.4.259

Offredi, 2003, De novo backbone and sequence design of an idealized alpha/beta-barrel protein: Evidence of stable tertiary structure, J. Mol. Biol., 325, 163, 10.1016/S0022-2836(02)01206-8

Teng, 2009, Modeling effects of human single nucleotide polymorphisms on protein-protein interactions, Biophys. J., 96, 2178, 10.1016/j.bpj.2008.12.3904

Theillet, 2013, The alphabet of intrinsic disorder, Intrinsically Disord. Proteins, 1, e24360, 10.4161/idp.24360

Basu, 2017, Proteus: A random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins, J. Comput. Aided Mol. Des., 31, 453, 10.1007/s10822-017-0020-y

Teilum, 2015, Globular and disordered—The non-identical twins in protein-protein interactions, Front. Mol. Biosci., 2, 40, 10.3389/fmolb.2015.00040

Linding, 2004, A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins, J. Mol. Biol., 342, 345, 10.1016/j.jmb.2004.06.088

Yoneda, 2017, Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation, Protein Sci., 26, 718, 10.1002/pro.3118

Marsh, 2006, Sensitivity of secondary structure propensities to sequence differences between α- and γ-synuclein: Implications for fibrillation, Protein Sci., 15, 2795, 10.1110/ps.062465306

Jahn, 2008, Folding versus aggregation: Polypeptide conformations on competing pathways, Arch. Biochem. Biophys., 469, 100, 10.1016/j.abb.2007.05.015

Uversky, 2010, Mysterious oligomerization of the amyloidogenic proteins, FEBS J., 277, 2940, 10.1111/j.1742-4658.2010.07721.x

Vacic, 2012, Disease mutations in disordered regions–exception to the rule?, Mol. Biosyst., 8, 27, 10.1039/C1MB05251A

Mechanic, 2005, Polymorphisms in XPD and TP53 and mutation in human lung cancer, Carcinogenesis, 26, 597, 10.1093/carcin/bgh344

Joerger, 2007, Structural biology of the tumor suppressor p53 and cancer-associated mutants, Adv. Cancer Res., 97, 1, 10.1016/S0065-230X(06)97001-8

Bullock, 1997, Thermodynamic stability of wild-type and mutant p53 core domain, Proc. Natl. Acad. Sci. USA, 94, 14338, 10.1073/pnas.94.26.14338

Feyfant, 2007, Modeling mutations in protein structures, Protein Sci., 16, 2030, 10.1110/ps.072855507

Studer, 2013, Residue mutations and their impact on protein structure and function: Detecting beneficial and pathogenic changes, Biochem. J., 449, 581, 10.1042/BJ20121221

Topham, 2013, Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase, Protein Sci., 22, 1754, 10.1002/pro.2375

Gerton, 1998, Effects of Mutations in Residues near the Active Site of Human Immunodeficiency Virus Type 1 Integrase on Specific Enzyme-Substrate Interactions, J. Virol., 72, 5046, 10.1128/JVI.72.6.5046-5055.1998

Woods, K.N., Pfeffer, J., Dutta, A., and Klein-Seetharaman, J. (2016). Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors. Sci. Rep., 6.

Luk, 2013, Unraveling the role of protein dynamics in dihydrofolate reductase catalysis, Proc. Natl. Acad. Sci. USA, 110, 16344, 10.1073/pnas.1312437110

Dixit, A., Yi, L., Gowthaman, R., Torkamani, A., Schork, N.J., and Verkhivker, G.M. (2009). Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases. PLoS ONE, 4.

Tyukhtenko, 2018, Effects of Distal Mutations on the Structure, Dynamics and Catalysis of Human Monoacylglycerol Lipase, Sci. Rep., 8, 1719, 10.1038/s41598-017-19135-7

Murphy, 2012, Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment, Biochemistry, 51, 8829, 10.1021/bi300783t

Souza, V.P., Ikegami, C.M., Arantes, G.M., and Marana, S.R. (2018). Mutations close to a hub residue affect the distant active site of a GH1 β-glucosidase. PLoS ONE, 13.

Kucukkal, 2015, Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins, Curr. Opin. Struct. Biol., 32, 18, 10.1016/j.sbi.2015.01.003

Peng, 2016, Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding, Proteins, 84, 232, 10.1002/prot.24968

Petukh, 2015, On human disease-causing amino acid variants: Statistical study of sequence and structural patterns, Hum. Mutat., 36, 524, 10.1002/humu.22770

Monticone, 2015, A case of severe hyperaldosteronism caused by a de novo mutation affecting a critical salt bridge Kir3.4 residue, J. Clin. Endocrinol. Metab., 100, E114, 10.1210/jc.2014-3636

Capriotti, 2004, A neural-network-based method for predicting protein stability changes upon single point mutations, Bioinformatics, 20, i63, 10.1093/bioinformatics/bth928

Capriotti, 2005, I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure, Nucleic Acids Res., 33, W306, 10.1093/nar/gki375

Pires, 2014, DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach, Nucleic Acids Res., 42, W314, 10.1093/nar/gku411

Pires, 2014, mCSM: Predicting the effects of mutations in proteins using graph-based signatures, Bioinformatics, 30, 335, 10.1093/bioinformatics/btt691

Worth, 2011, SDM–A server for predicting effects of mutations on protein stability and malfunction, Nucleic Acids Res., 39, W215, 10.1093/nar/gkr363

Blanco, 2018, FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1), Nucleic Acids Res., 46, 3852, 10.1093/nar/gky228

Schymkowitz, 2005, The FoldX web server: An online force field, Nucleic Acids Res., 33, W382, 10.1093/nar/gki387

Zhang, 2012, Predicting folding free energy changes upon single point mutations, Bioinformatics, 28, 664, 10.1093/bioinformatics/bts005

Getov, I., Petukh, M., and Alexov, E. (2016). SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach. Int. J. Mol. Sci., 17.

Li, 2014, Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity, J. Chem. Theory Comput., 10, 1770, 10.1021/ct401022c

Petukh, M., Dai, L., and Alexov, E. (2016). SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations. Int. J. Mol. Sci., 17.

Cang, 2017, Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology, Bioinformatics, 33, 3549

Cang, Z., and Wei, G.-W. (2017). TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions. PLOS Comput. Biol., 13.

Knowles, 2007, Kinetics and thermodynamics of amyloid formation from direct measurements of fluctuations in fibril mass, Proc. Natl. Acad. Sci. USA, 104, 10016, 10.1073/pnas.0610659104

Rivas, 2016, Macromolecular crowding in vitro, in vivo, and in between, Trends Biochem. Sci., 41, 970, 10.1016/j.tibs.2016.08.013

Lee, 2015, Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme, Nucleic Acids Res., 43, 1170, 10.1093/nar/gku1335

Senske, 2014, Protein Stabilization by Macromolecular Crowding through Enthalpy Rather Than Entropy, J. Am. Chem. Soc., 136, 9036, 10.1021/ja503205y

Vreven, 2012, Prediction of protein–protein binding free energies, Protein Sci., 21, 396, 10.1002/pro.2027

Hedger, 2017, Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association, J. Phys. Chem. B, 121, 3364, 10.1021/acs.jpcb.6b08445

Henriksen, 2015, Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics, J. Chem. Theory Comput., 11, 4377, 10.1021/acs.jctc.5b00405

Lodish, H., Berk, A., Zipursky, S.L., Matsudaira, P., Baltimore, D., and Darnell, J. (2019, December 22). Mutations: Types and Causes. Molecular Cell Biology 4th Edition 2000, Available online: https://www.ncbi.nlm.nih.gov/books/NBK21578/.

Gao, 2015, Insights into disease-associated mutations in the human proteome through protein structural analysis, Structure, 23, 1362, 10.1016/j.str.2015.03.028

Casadio, 2011, Correlating disease-related mutations to their effect on protein stability: A large-scale analysis of the human proteome, Hum. Mutat., 32, 1161, 10.1002/humu.21555

Adzhubei, 2010, A method and server for predicting damaging missense mutations, Nat. Methods, 7, 248, 10.1038/nmeth0410-248

Hughes, 2011, Principles of early drug discovery, Br. J. Pharmacol., 162, 1239, 10.1111/j.1476-5381.2010.01127.x

Michel, 2014, Current and emerging opportunities for molecular simulations in structure-based drug design, Phys. Chem. Chem. Phys., 16, 4465, 10.1039/C3CP54164A

Hung, 2014, Computational approaches for drug discovery, Drug Dev. Res., 75, 412, 10.1002/ddr.21222

Lounnas, V., Ritschel, T., Kelder, J., McGuire, R., Bywater, R.P., and Foloppe, N. (2013). Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery. Comput. Struct. Biotechnol. J., 5.

Sawicki, 1993, Human Genome Project, Am. J. Surg., 165, 258, 10.1016/S0002-9610(05)80522-7

(2010). The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.

Peng, Y., Norris, J., Schwartz, C., and Alexov, E. (2016). Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase. Int. J. Mol. Sci., 17.

Li, 2017, Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations, Sci. Rep., 7, 8237, 10.1038/s41598-017-08419-7

Spellicy, 2018, Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects, Eur. J. Hum. Genet., 26, 420, 10.1038/s41431-017-0025-y

Vaidyanathan, 2017, Identification and characterization of a missense mutation in the O-linked β-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability, J. Biol. Chem., 292, 8948, 10.1074/jbc.M116.771030

Chen, W.-T., Hong, C.-J., Lin, Y.-T., Chang, W.-H., Huang, H.-T., Liao, J.-Y., Chang, Y.-J., Hsieh, Y.-F., Cheng, C.-Y., and Liu, H.-C. (2012). Amyloid-beta (Aβ) D7H mutation increases oligomeric Aβ42 and alters properties of Aβ-zinc/copper assemblies. PLoS ONE, 7.

Alexov, E. (2019, January 08). Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine. Available online: https://www.hindawi.com/journals/ab/2014/471836/.

Yang, 2016, Binding Analysis of Methyl-CpG Binding Domain of MeCP2 and Rett Syndrome Mutations, ACS Chem. Biol., 11, 2706, 10.1021/acschembio.6b00450

Peng, Y., Myers, R., Zhang, W., and Alexov, E. (2018). Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome. Int. J. Mol. Sci., 19.

Peng, 2015, Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease, Int. J. Mol. Sci., 16, 27270, 10.3390/ijms161126022

Ferreira, 2015, Molecular docking and structure-based drug design strategies, Molecules, 20, 13384, 10.3390/molecules200713384

Bleicher, 2003, Hit and lead generation: Beyond high-throughput screening, Nat. Rev. Drug Discov., 2, 369, 10.1038/nrd1086

Lang, 2009, DOCK 6: Combining techniques to model RNA-small molecule complexes, RNA, 15, 1219, 10.1261/rna.1563609

Trott, 2010, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J. Comput. Chem., 31, 455, 10.1002/jcc.21334

Friesner, 2004, Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J. Med. Chem., 47, 1739, 10.1021/jm0306430

Jain, 2003, Surflex:  Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine, J. Med. Chem., 46, 499, 10.1021/jm020406h

Nair, 2014, Molecular dynamics simulations: From structure function relationships to drug discovery, In Silico Pharmacol, 2, 4, 10.1186/s40203-014-0004-8

Vogelstein, 2000, Surfing the p53 network, Nature, 408, 307, 10.1038/35042675

Hollstein, 1991, p53 mutations in human cancers, Science, 253, 49, 10.1126/science.1905840

Muller, 2014, Mutant p53 in Cancer: New Functions and Therapeutic Opportunities, Cancer Cell, 25, 304, 10.1016/j.ccr.2014.01.021

Bullock, 2001, Rescuing the function of mutant p53, Nat. Rev. Cancer, 1, 68, 10.1038/35094077

Wassman, 2013, Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53, Nat. Commun., 4, 1407, 10.1038/ncomms2361

Kaar, 2010, Stabilization of mutant p53 via alkylation of cysteines and effects on DNA binding, Protein Sci., 19, 2267, 10.1002/pro.507

Pegg, 2010, Spermine synthase, Cell. Mol. Life Sci., 67, 113, 10.1007/s00018-009-0165-5

Zhang, Z., Martiny, V., Lagorce, D., Ikeguchi, Y., Alexov, E., and Miteva, M.A. (2014). Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual Screening and Free Energy-Based Approach. PLoS ONE, 9.

Zhang, 2013, A rational free energy-based approach to understanding and targeting disease-causing missense mutations, J. Am. Med. Inform. Assoc., 20, 643, 10.1136/amiajnl-2012-001505

Dror, 2009, Novel approach for efficient pharmacophore-based virtual screening: Method and applications, J. Chem. Inf. Model., 49, 2333, 10.1021/ci900263d

Kaserer, 2015, Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases, Molecules, 20, 22799, 10.3390/molecules201219880

Lee, 2011, Reviewing ligand-based rational drug design: The search for an ATP synthase inhibitor, Int. J. Mol. Sci., 12, 5304, 10.3390/ijms12085304

Chen, 2009, Pharmacophore-based virtual screening versus docking-based virtual screening: A benchmark comparison against eight targets, Acta Pharmacol. Sin., 30, 1694, 10.1038/aps.2009.159

Singh, 2018, Molecular dynamics guided development of indole based dual inhibitors of EGFR (T790M) and c-MET, Bioorg. Chem., 79, 163, 10.1016/j.bioorg.2018.04.001

Springsteel, 2003, Benzoflavone activators of the cystic fibrosis transmembrane conductance regulator: Towards a pharmacophore model for the nucleotide-binding domain, Bioorg. Med. Chem., 11, 4113, 10.1016/S0968-0896(03)00435-8

Pathak, 2016, Identification of non-resistant ROS-1 inhibitors using structure based pharmacophore analysis, J. Mol. Graph. Model., 70, 85, 10.1016/j.jmgm.2016.09.013

Wang, 2017, Discovery of (R)-1-(3-(4-Amino-3-(3-chloro-4-(pyridin-2-ylmethoxy)phenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one (CHMFL-EGFR-202) as a Novel Irreversible EGFR Mutant Kinase Inhibitor with a Distinct Binding Mode, J. Med. Chem., 60, 2944, 10.1021/acs.jmedchem.6b01907

Goldstraw, 2011, Non-small-cell lung cancer, Lancet, 378, 1727, 10.1016/S0140-6736(10)62101-0

Awad, 2013, Acquired Resistance to Crizotinib from a Mutation in CD74–ROS1, N. Engl. J. Med., 368, 2395, 10.1056/NEJMoa1215530

Acharya, 2011, Recent advances in ligand-based drug design: Relevance and utility of the conformationally sampled pharmacophore approach, Curr. Comput. Aided Drug Des., 7, 10, 10.2174/157340911793743547

Kerem, 1989, Identification of the cystic fibrosis gene: Genetic analysis, Science, 245, 1073, 10.1126/science.2570460

Noy, 2011, Combating cystic fibrosis: In search for CF transmembrane conductance regulator (CFTR) modulators, ChemMedChem, 6, 243, 10.1002/cmdc.201000488

Liessi, 2018, Synthesis and biological evaluation of novel thiazole- VX-809 hybrid derivatives as F508del correctors by QSAR-based filtering tools, Eur. J. Med. Chem., 144, 179, 10.1016/j.ejmech.2017.12.030

Wilson, 2011, Integrating structure-based and ligand-based approaches for computational drug design, Future Med. Chem., 3, 735, 10.4155/fmc.11.18

Drwal, 2013, Combination of ligand- and structure-based methods in virtual screening, Drug Discov. Today Technol., 10, e395, 10.1016/j.ddtec.2013.02.002

Konrat, 2009, The protein meta-structure: A novel concept for chemical and molecular biology, Cell. Mol. Life Sci., 66, 3625, 10.1007/s00018-009-0117-0

Naranjo, 2012, Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins, Mol. Biosyst., 8, 411, 10.1039/C1MB05367A

Koch, 2005, Protein structure similarity clustering and natural product structure as guiding principles in drug discovery, Drug Discov. Today, 10, 471, 10.1016/S1359-6446(05)03419-7

Pandurangan, 2017, Genomes, structural biology and drug discovery: Combating the impacts of mutations in genetic disease and antibiotic resistance, Biochem. Soc. Trans., 45, 303, 10.1042/BST20160422

Zhang, Z., Norris, J., Schwartz, C., and Alexov, E. (2011). In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in Spermine Synthase. PLoS ONE, 6.

Frey, 2010, Predicting resistance mutations using protein design algorithms, Proc. Natl. Acad. Sci. USA, 107, 13707, 10.1073/pnas.1002162107

Gilchrist, S., Gilbert, N., Perry, P., Östlund, C., Worman, H.J., and Bickmore, W.A. (2004). Altered protein dynamics of disease-associated lamin A mutants. BMC Cell. Biol., 5.

Ferreira, 2001, PABMB Lecture. Protein dynamics, folding and misfolding: From basic physical chemistry to human conformational diseases, FEBS Lett., 498, 129, 10.1016/S0014-5793(01)02491-7

Cheng, 2008, Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase, J. Med. Chem., 51, 3878, 10.1021/jm8001197

Ostermeier, 1997, Crystallization of membrane proteins, Curr. Opin. Struct. Biol., 7, 697, 10.1016/S0959-440X(97)80080-2

Lluis, 2013, Protein engineering methods applied to membrane protein targets, Protein Eng. Des. Sel., 26, 91, 10.1093/protein/gzs079

Amaro, 2008, An improved relaxed complex scheme for receptor flexibility in computer-aided drug design, J. Comput. Aided Mol. Des., 22, 693, 10.1007/s10822-007-9159-2

Yu, 2016, Structure-based Inhibitor Design for the Intrinsically Disordered Protein c-Myc, Sci. Rep., 6, 22298, 10.1038/srep22298

Chen, 2013, How to design a drug for the disordered proteins?, Drug Discov. Today, 18, 910, 10.1016/j.drudis.2013.04.008

Yin, 2016, Drugging Membrane Protein Interactions, Annu. Rev. Biomed. Eng., 18, 51, 10.1146/annurev-bioeng-092115-025322

Saven, 2012, Computational Design of Membrane Proteins, Structure, 20, 5, 10.1016/j.str.2011.12.003

Alford, R.F., Koehler Leman, J., Weitzner, B.D., Duran, A.M., Tilley, D.C., Elazar, A., and Gray, J.J. (2015). An Integrated Framework Advancing Membrane Protein Modeling and Design. PLoS Comput. Biol., 11.

Patra, H.K., Islam, M., Basu, S., and Griffith, M. Peptide Architectonics for Biotherapeutics. (Application No. 201741036721), Indian Patent, Filed on 16 October 2017.