Multi-state design of flexible proteins predicts sequences optimal for conformational change

E Humphris-Narayanan, 2012, Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design, PLoS Comput Biol, 8, e1002639, 10.1371/journal.pcbi.1002639

EA Christian, 2013, Atomic-level functional model of dengue virus Envelope protein infectivity, Proc Natl Acad Sci U S A, 110, 18662, 10.1073/pnas.1310962110

CA Smith, 2008, Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction, J Mol Biol, 380, 742, 10.1016/j.jmb.2008.05.023

CA Smith, 2011, Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design, PloS one, 6, e20451, 10.1371/journal.pone.0020451

SY Rhee, 2003, Human immunodeficiency virus reverse transcriptase and protease sequence database, Nucleic Acids Res, 31, 298, 10.1093/nar/gkg100

GD Friedland, 2009, correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family, PLoS Comput Biol, 5, e1000393, 10.1371/journal.pcbi.1000393

JA Davey, 2012, Multistate approaches in computational protein design, Protein science: a publication of the Protein Society, 21, 1241, 10.1002/pro.2128

M Fromer, 2009, Tradeoff between stability and multispecificity in the design of promiscuous proteins, PLoS Comput Biol, 5, e1000627, 10.1371/journal.pcbi.1000627

BD Allen, 2010, An efficient algorithm for multistate protein design based on FASTER, Journal of computational chemistry, 31, 904, 10.1002/jcc.21375

A Leaver-Fay, 2011, A generic program for multistate protein design, PloS one, 6, e20937, 10.1371/journal.pone.0020937

EL Humphris, 2007, Design of multi-specificity in protein interfaces, PLoS Comput Biol, 3, e164, 10.1371/journal.pcbi.0030164

AM Sevy, 2015, Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences, PLoS Comput Biol, 11, e1004300, 10.1371/journal.pcbi.1004300

AM Sevy, 2019, Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses, Proc Natl Acad Sci U S A, 116, 1597, 10.1073/pnas.1806004116

AT Heiny, 2007, Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets, PloS one, 2, e1190, 10.1371/journal.pone.0001190

F Friedberg, 2001, Evolutionary aspects of calmodulin, IUBMB Life, 51, 215, 10.1080/152165401753311753

M Kobayashi, 2004, Conservation of functional domain structure in bicarbonate-regulated "soluble" adenylyl cyclases in bacteria and eukaryotes, Dev Genes Evol, 214, 503

RT Shealy, 2003, Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure, Biophysical journal, 84, 2929, 10.1016/S0006-3495(03)70020-4

T Hrabe, 2016, PDBFlex: exploring flexibility in protein structures, Nucleic Acids Res, 44, D423, 10.1093/nar/gkv1316

A Stein, 2013, Improvements to robotics-inspired conformational sampling in rosetta, PloS one, 8, e63090, 10.1371/journal.pone.0063090

I Kufareva, 2012, Methods of protein structure comparison, Methods in molecular biology, 857, 231, 10.1007/978-1-61779-588-6_10

O Carugo, 2001, A normalized root-mean-square distance for comparing protein three-dimensional structures, Protein science: a publication of the Protein Society, 10, 1470, 10.1110/ps.690101

HBa Mann, 1947, On a test whether one or two random variables is stochastically larger than the other, The Annals of Mathematical Statistics, 18, 50, 10.1214/aoms/1177730491

MG Kendall, 1948, Rank Correlation Methods, 160

M Sternke, 2019, Consensus sequence design as a general strategy to create hyperstable, biologically active proteins, Proc Natl Acad Sci U S A, 116, 11275, 10.1073/pnas.1816707116

DB Halling, 2016, Conserved properties of individual Ca2+-binding sites in calmodulin, Proc Natl Acad Sci U S A, 113, E1216, 10.1073/pnas.1600385113

Y Bao, 2008, The influenza virus resource at the National Center for Biotechnology Information, J Virol, 82, 596, 10.1128/JVI.02005-07

WI Weis, 1990, Refinement of the influenza virus hemagglutinin by simulated annealing, J Mol Biol, 212, 737, 10.1016/0022-2836(90)90234-D

RJ Russell, 2008, Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion, Proc Natl Acad Sci U S A, 105, 17736, 10.1073/pnas.0807142105

J Chen, 1999, N- and C-terminal residues combine in the fusion-pH influenza hemagglutinin HA(2) subunit to form an N cap that terminates the triple-stranded coiled coil, Proc Natl Acad Sci U S A, 96, 8967, 10.1073/pnas.96.16.8967

PA Bullough, 1994, Structure of influenza haemagglutinin at the pH of membrane fusion, Nature, 371, 37, 10.1038/371037a0

Y Zhou, 2009, Viral calciomics: interplays between Ca2+ and virus, Cell Calcium, 46, 1, 10.1016/j.ceca.2009.05.005

DC Ekiert, 2011, A highly conserved neutralizing epitope on group 2 influenza A viruses, Science, 333, 843, 10.1126/science.1204839

H Levene, 1960, Robust tests for equality of variances, 517

Student, 1908, The probable error of a mean, Biometrika, 6, 1, 10.2307/2331554

A Leaver-Fay, 2011, ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules, Methods in enzymology, 487, 545, 10.1016/B978-0-12-381270-4.00019-6

A Zemla, 2003, LGA: A method for finding 3D similarities in protein structures, Nucleic Acids Res, 31, 3370, 10.1093/nar/gkg571

RA Abagyan, 1997, Contact area difference (CAD): a robust measure to evaluate accuracy of protein models, J Mol Biol, 268, 678, 10.1006/jmbi.1997.0994

B Marsden, 2004, SAD—a normalized structural alignment database: improving sequence-structure alignments, Bioinformatics, 20, 2333, 10.1093/bioinformatics/bth244

KF O’Rourke, 2016, Biophysical and computational methods to analyze amino acid interaction networks in proteins, Comput Struct Biotechnol J, 14, 245, 10.1016/j.csbj.2016.06.002

OF Lange, 2008, Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution, Science, 320, 1471, 10.1126/science.1157092

JA Davey, 2017, Multistate Computational Protein Design with Backbone Ensembles, Methods in molecular biology, 1529, 161, 10.1007/978-1-4939-6637-0_7

JR Brender, 2017, An Evolution-Based Approach to De Novo Protein Design, Methods in molecular biology, 1529, 243, 10.1007/978-1-4939-6637-0_12

F Tsai, 2017, Bim suppresses the development of SLE by limiting myeloid inflammatory responses, J Exp Med, 214, 3753, 10.1084/jem.20170479

B Thyagarajan, 2014, The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin, eLife, 3, 10.7554/eLife.03300

F Morcos, 2011, Direct-coupling analysis of residue coevolution captures native contacts across many protein families, Proc Natl Acad Sci U S A, 108, E1293, 10.1073/pnas.1111471108

GB Gloor, 2005, Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions, Biochemistry, 44, 7156, 10.1021/bi050293e

ER Tillier, 2003, Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments, Bioinformatics, 19, 750, 10.1093/bioinformatics/btg072

LC Martin, 2005, Using information theory to search for co-evolving residues in proteins, Bioinformatics, 21, 4116, 10.1093/bioinformatics/bti671

U Gobel, 1994, Correlated mutations and residue contacts in proteins, Proteins, 18, 309, 10.1002/prot.340180402

O Olmea, 1999, Effective use of sequence correlation and conservation in fold recognition, J Mol Biol, 293, 1221, 10.1006/jmbi.1999.3208

D de Juan, 2013, Emerging methods in protein co-evolution, Nat Rev Genet, 14, 249, 10.1038/nrg3414

SA Combs, 2013, Small-molecule ligand docking into comparative models with Rosetta, Nature protocols, 8, 1277, 10.1038/nprot.2013.074

GE Crooks, 2004, WebLogo: a sequence logo generator, Genome research, 14, 1188, 10.1101/gr.849004

CE Shannon, 1997, The mathematical theory of communication. 1963, MD Comput, 14, 306

JR Willis, 2013, Human germline antibody gene segments encode polyspecific antibodies, PLoS Comput Biol, 9, e1003045, 10.1371/journal.pcbi.1003045

NA Weiss, 2005, A Course in Probability

LY Yampolsky, 2005, The exchangeability of amino acids in proteins, Genetics, 170, 1459, 10.1534/genetics.104.039107

F Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Molecular systems biology, 7, 539, 10.1038/msb.2011.75

F Sievers, 2018, Clustal Omega for making accurate alignments of many protein sequences, Protein science: a publication of the Protein Society, 27, 135, 10.1002/pro.3290

E Durham, 2009, Solvent accessible surface area approximations for rapid and accurate protein structure prediction, Journal of molecular modeling, 15, 1093, 10.1007/s00894-009-0454-9

S Ovchinnikov, 2014, Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information, eLife, 3, e02030, 10.7554/eLife.02030