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Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history.
Computer simulation of protein folding
Levitt M · 1975
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The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
Marquart M · 1983
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Chymotrypsin: molecular and catalytic properties
Appel W · 1986
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A learning algorithm for Boltzmann machines
Ackley DH · 1987
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Enumeration of all compact conformations of copolymers with random sequence of links
Shakhnovich E · 1990
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A conserved loop in the ATPase domain of the DnaK chaperone is essential for stable binding of GrpE
Buchberger A · 1994
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Rapid evolution of a protein in vitro by DNA shuffling
Stemmer WP · 1994
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Characterization of a novel protein-binding module—the WW domain
Sudol M · 1995
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VMD: visual molecular dynamics
Humphrey W · 1996
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Conversion of the Kunitz-type module of collagen VI into a highly active trypsin inhibitor by site-directed mutagenesis
Kohfeldt E · 1996
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Residue–residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
Miyazawa S · 1996
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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions1
Simons KT · 1997
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The Hsp70 and Hsp60 chaperone machines
Bukau B · 1998
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1.2 Å refinement of the Kunitz-type domain from the α \alpha 3 chain of human type VI collagen
Merigeau K · 1998
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A single point mutation in a group I WW domain shifts its specificity to that of group II WW domains
Espanel X · 1999
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Correlated mutations in models of protein sequences: phylogenetic and structural effects
Lapedes AS · 1999
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Bikunin—not just a plasma proteinase inhibitor
Fries E · 2000
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Inhibition of six serine proteinases of the human coagulation system by mutants of bovine pancreatic trypsin inhibitor
Grzesiak A · 2000
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Structural analysis of WW domains and design of a WW prototype
Macias MJ · 2000
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Protein interactions and ligand binding: from protein subfamilies to functional specificity
Rausell A · 2000
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Structure of TPR domain–peptide complexes: critical elements in the assembly of the Hsp70–Hsp90 multichaperone machine
Scheufler C · 2000
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NeW wrinkles for an old domain
Sudol M · 2000
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Structure and biology of tissue factor pathway inhibitor
Bajaj MS · 2001
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Tuning of chaperone activity of Hsp70 proteins by modulation of nucleotide exchange
Brehmer D · 2001
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Structural analysis of BAG1 cochaperone and its interactions with Hsc70 heat shock protein
Briknarová K · 2001
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The carboxyl terminus of type VII collagen mediates antiparallel-dimer formation and constitutes a new antigenic epitope for EBA autoantibodies
Chen M · 2001
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Protein Folding Theory: From Lattice to All-Atom Models
Mirny L · 2001
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Annealed importance sampling
Neal RM · 2001
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Structure of a Bag/Hsc70 complex: convergent functional evolution of Hsp70 nucleotide exchange factors
Sondermann H · 2001
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Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building
Kato Y · 2002
Cited alongside, same era.
The bovine basic pancreatic trypsin inhibitor (Kunitz inhibitor): a milestone protein
Ascenzi P · 2003
Cited alongside, same era.
Tissue expression, protease specificity, and Kunitz domain functions of hepatocyte growth factor activator inhibitor-1B (HAI-1B), a new splice variant of HAI-1
Kirchhofer D · 2003
Cited alongside, same era.
WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains
Otte L · 2003
Cited alongside, same era.
Structure function analysis of the reactive site in the first kunitz-type domain of human tissue factor pathway inhibitor-2
Chand HS · 2004
Cited alongside, same era.
Three-dimensional structures of membrane proteins from genomic sequencing
Hopf TA · 2012
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The Ras protein superfamily: evolutionary tree and role of conserved amino acids
Rojas AM · 2012
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Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
Teppa E · 2012
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From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction
Cocco S · 2013
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Emerging methods in protein co-evolution
De Juan D · 2013
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Pfam: the protein families database
Finn RD · 2013
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A family of evolution–entropy hybrid methods for ranking protein residues by importance
Mihalek I · 2004
Cited alongside, same era.
Pathways of chaperone-mediated protein folding in the cytosol
Young JC · 2004
Cited alongside, same era.
Natural-like function in artificial WW domains
Russ WP · 2005
Cited alongside, same era.
Structure–function–folding relationship in a WW domain
Jäger M · 2006
Cited alongside, same era.
Determinants of protein function revealed by combinatorial entropy optimization
Reva B · 2007
Cited alongside, same era.
Representational power of restricted Boltzmann machines and deep belief networks
Le Roux N · 2008
Cited alongside, same era.
On the quantitative analysis of deep belief networks
Salakhutdinov R · 2008
Cited alongside, same era.
Later among the works it cites.
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence-and structure-rich era
Kamisetty H · 2013
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Auto-encoding variational bayes
Kingma DP · 2013
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Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP
Qi R · 2013
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Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
Ekeberg M · 2014
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Improving contact prediction along three dimensions
Feinauer C · 2014
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Generative adversarial nets
Goodfellow I · 2014
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The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing
Mann JK · 2014
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Intrinsically disordered proteins and intrinsically disordered protein regions
Oldfield CJ · 2014
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Large-scale conformational transitions and dimerization are encoded in the amino-acid sequences of Hsp70 chaperones
Malinverni D · 2015
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From residue coevolution to protein conformational ensembles and functional dynamics
Sutto L · 2015
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ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
Ashkenazy H · 2016
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Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1
Figliuzzi M · 2016
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Benchmarking inverse statistical approaches for protein structure and design with exactly solvable models
Jacquin H · 2016
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Why reinvent the wheel? Building new proteins based on ready-made parts
Khersonsky O · 2016
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Mutation effects predicted from sequence co-variation
Hopf TA · 2017
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Deep generative models of genetic variation capture mutation effects
Riesselman AJ · 2017
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Variational auto-encoding of protein sequences
Sinai S · 2017
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Emergence of compositional representations in restricted Boltzmann machines
Tubiana J · 2017
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The remarkable multivalency of the Hsp70 chaperones
Zuiderweg ER · 2017
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Inverse statistical physics of protein sequences: A key issues review
Cocco S · 2018
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Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs
Haldane A · 2018
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Efficient sampling and parametrization improve Restricted Boltzmann Machines
Tubiana J · 2018
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