相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Fine tuning of receptor-selectivity for tumor necrosis factor-α using a phage display system with one-step competitive panning
Yasuhiro Abe et al.
BIOMATERIALS (2011)
Protein binding specificity versus promiscuity
Gideon Schreiber et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Optimization of Combinatorial Mutagenesis
Andrew S. Parker et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2011)
Design of Peptide Inhibitors That Bind the bZIP Domain of Epstein-Barr Virus Protein BZLF1
T. Scott Chen et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
Determinants of Homodimerization Specificity in Histidine Kinases
Orr Ashenberg et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution
Olga Khersonsky et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
A De Novo Protein Binding Pair By Computational Design and Directed Evolution
John Karanicolas et al.
MOLECULAR CELL (2011)
The multiple-specificity landscape of modular peptide recognition domains
David Gfeller et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Automated minimization of steric clashes in protein structures
Srinivas Ramachandran et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Triathlon for energy functions: Who is the winner for design of protein-protein interactions?
Oz Sharabi et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
Sarel J. Fleishman et al.
SCIENCE (2011)
Evolving specificity from variability for protein interaction domains
Tomonori Kaneko et al.
TRENDS IN BIOCHEMICAL SCIENCES (2011)
Identification of bZIP Interaction Partners of Viral Proteins HBZ, MEQ, BZLF1, and K-bZIP Using Coiled-Coil Arrays
Aaron W. Reinke et al.
BIOCHEMISTRY (2010)
Engineering Signal Transduction Pathways
Christina Kiel et al.
CELL (2010)
PDZ domains and their binding partners: structure, specificity, and modification
Ho-Jin Lee et al.
CELL COMMUNICATION AND SIGNALING (2010)
Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library
Shaun M. Lippow et al.
CHEMISTRY & BIOLOGY (2010)
mRNA display selection of a high-affinity, Bcl-XL-specific binding peptide
Nobutaka Matsumura et al.
FASEB JOURNAL (2010)
Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains
Colin A. Smith et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Determinants of BH3 Binding Specificity for Mcl-1 versus BcI-xL
Sanjib Dutta et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
SH2 Domains Recognize Contextual Peptide Sequence Information to Determine Selectivity
Bernard A. Liu et al.
MOLECULAR & CELLULAR PROTEOMICS (2010)
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing
Andreas Ernst et al.
MOLECULAR BIOSYSTEMS (2010)
Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles
Benjamin D. Allen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction
Nicola A. G. Meenan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Engineering a protein-protein interface using a computationally designed library
Gurkan Guntas et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries
Roberto A. Chica et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Creating novel proteins by combining design and selection
Tijana Z. Grove et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2010)
Computational design of second-site suppressor mutations at protein-protein interfaces
Deanne W. Sammond et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Loops Govern SH2 Domain Specificity by Controlling Access to Binding Pockets
Tomonori Kaneko et al.
SCIENCE SIGNALING (2010)
Backbone flexibility in computational protein design
Daniel J. Mandell et al.
CURRENT OPINION IN BIOTECHNOLOGY (2009)
Advances in generating functional diversity for directed protein evolution
Amol V. Shivange et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2009)
Computational design of affinity and specificity at protein-protein interfaces
John Karanicolas et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability
Pete Heinzelman et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2009)
Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity
Eliyahu Yosef et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Insights into Positive and Negative Requirements for Protein-Protein Interactions by Crystallographic Analysis of the β-Lactamase Inhibitory Proteins BLIP, BLIP-1, and BLP
Michael Gretes et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Design of protein-interaction specificity gives selective bZIP-binding peptides
Gevorg Grigoryan et al.
NATURE (2009)
Computer-aided design of functional protein interactions
Daniel J. Mandell et al.
NATURE CHEMICAL BIOLOGY (2009)
Predicting free energy changes using structural ensembles
Alexander Benedix et al.
NATURE METHODS (2009)
'Edgetic' perturbation of a C. elegans BCL2 ortholog
Matija Dreze et al.
NATURE METHODS (2009)
Following evolutionary paths to protein-protein interactions with high affinity and selectivity
Kalia Bernath Levin et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)
Protein design in biological networks: from manipulating the input to modifying the output
Almer M. Van der Sloot et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2009)
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
Vladimir Potapov et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2009)
Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins
Raffi Tonikian et al.
PLOS BIOLOGY (2009)
Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins
Menachem Fromer et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Macromolecular modeling with Rosetta
Rhiju Das et al.
ANNUAL REVIEW OF BIOCHEMISTRY (2008)
Protein design by directed evolution
Christian Jaeckel et al.
ANNUAL REVIEW OF BIOPHYSICS (2008)
Algorithm for backrub motions in protein design
Ivelin Georgiev et al.
BIOINFORMATICS (2008)
Rewiring the specificity of two-component signal transduction systems
Jeffrey M. Skerker et al.
CELL (2008)
A novel BH3 ligand that selectively targets Mcl-1 reveals that apoptosis can proceed without Mcl-1 degradation
Erinna F. Lee et al.
JOURNAL OF CELL BIOLOGY (2008)
The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
Ivelin Georgiev et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing
Mingyang Lu et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Computational Redesign of a Protein-Protein Interface for High Affinity and Binding Specificity Using Modular Architecture and Naturally Occurring Template Fragments
V. Potapov et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
Colin A. Smith et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Targeting metastable coiled-coil domains by computational design
Patrick Barth et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Kemp elimination catalysts by computational enzyme design
Daniela Rothlisberger et al.
NATURE (2008)
Predicting PDZ domain-peptide interactions from primary sequences
Jiunn R. Chen et al.
NATURE BIOTECHNOLOGY (2008)
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions
Jianhan Chen et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
Aviva Presser et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Evaluating and optimizing computational protein design force fields using fixed composition-based negative design
Oscar Alvizo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Affinity maturation of antibodies assisted by in silico modeling
Rodrigo Barderas et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Hydrophile scanning as a complement to alanine scanning for exploring and manipulating protein-protein recognition: Application to the Bim BH3 domain
Melissa D. Boersma et al.
PROTEIN SCIENCE (2008)
Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics
Caleb J. Bashor et al.
SCIENCE (2008)
A specificity map for the PDZ domain family
Raffi Tonikian et al.
PLOS BIOLOGY (2008)
A knowledge-based forcefield for protein-protein interface design
Louis A. Clark et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
Modeling backbone flexibility improves protein stability estimation
Shuangye Yin et al.
STRUCTURE (2007)
Computational design of antibody-affinity improvement beyond in vivo maturation
Shaun M. Lippow et al.
NATURE BIOTECHNOLOGY (2007)
Structural basis of Dscam isoform specificity
Rob Meijers et al.
NATURE (2007)
A vast repertoire of Dscam binding Specificities arises from modular interactions of variable ig domains
Woj M. Wojtowicz et al.
CELL (2007)
Structure-based protocol for identifying mutations that enhance protein-protein binding affinities
Deanne W. Sammond et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Modeling backbone flexibility to achieve sequence diversity: The design of novel a-helical ligands for Bcl-XL
Xiaoran Fu et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Phage display for engineering and analyzing protein interaction interfaces
Sachdev S. Sidhu et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)
Optimal protein library design using recombination or point mutations based on sequence-based scoring functions
Robert J. Pantazes et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2007)
Progress in computational protein design
Shaun M. Lippow et al.
CURRENT OPINION IN BIOTECHNOLOGY (2007)
PDZ domain binding selectivity is optimized across the mouse proteome
Michael A. Stiffler et al.
SCIENCE (2007)
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases
Michal Szczepek et al.
NATURE BIOTECHNOLOGY (2007)
Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
Yaping Feng et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Positive aspects of negative design:: Simultaneous selection of specificity and interaction stability
Jody M. Mason et al.
BIOCHEMISTRY (2007)
Potential energy functions for protein design
F. Edward Boas et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)
Accurate, conformation-dependent predictions of solvent effects on protein ionization constants
P. Barth et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function
Thomas P. Treynor et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Statistical potential for assessment and prediction of protein structures
Min-Yi Shen et al.
PROTEIN SCIENCE (2006)
Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide
David F. Green et al.
BIOCHEMISTRY (2006)
Stability of 100 homo and heterotypic coiled-coil a-a′ pairs for ten amino acids ( A, L, I, V, N, K, S, T, E, and R)
Asha Acharya et al.
BIOCHEMISTRY (2006)
Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1 - Insights into determinants of PDZ domain specificity
Brent A. Appleton et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
Semirational design of Jun-Fos coiled coils with increased affinity:: Universal implications for leucine zipper prediction and design
Jody M. Mason et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor
Almer M. van der Sloot et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Ultra-fast evaluation of protein energies directly from sequence
Gevorg Grigoryan et al.
PLOS COMPUTATIONAL BIOLOGY (2006)
IPRO: An iterative computational protein library redesign and optimization procedure
Manish C. Saraf et al.
BIOPHYSICAL JOURNAL (2006)
Structure-guided recombination creates an artificial family of cytochromes P450
Christopher R. Otey et al.
PLOS BIOLOGY (2006)
In quest of an empirical potential for protein structure prediction
J Skolnick
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
Proteome survey reveals modularity of the yeast cell machinery
AC Gavin et al.
NATURE (2006)
Structure-based prediction of bZIP partnering specificity
G Grigoryan et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Deciphering B-ZIP transcription factor interactions in vitro and in vivo
Charles Vinson et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION (2006)
Antibody diversification - Mutational mechanisms and oncogenesis
Darina Frieder et al.
IMMUNOLOGIC RESEARCH (2006)
Optimizing the affinity and specificity of proteins with molecular display
AM Levin et al.
MOLECULAR BIOSYSTEMS (2006)
Automated design of degenerate codon libraries
MA Mena et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2005)
Towards a proteome-scale map of the human protein-protein interaction network
JF Rual et al.
NATURE (2005)
An atomic environment potential for use in protein structure prediction
CM Summa et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Specificity versus stability in computational protein design
DN Bolon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Solving and analyzing side-chain positioning problems using linear and integer programming
CL Kingsford et al.
BIOINFORMATICS (2005)
Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
N Pokala et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function
L Chen et al.
MOLECULAR CELL (2005)
Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed α/β structure
MH Ali et al.
STRUCTURE (2005)
Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: Scope and mechanism
TJ Magliery et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Computational redesign of protein-protein interaction specificity
T Kortemme et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)
Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: A protein-design study
DN Bolon et al.
MOLECULAR CELL (2004)
The organization and evolution of the Dipteran and Hymenopteran Down syndrome cell adhesion molecule (Dscam) genes
BR Graveley et al.
RNA (2004)
Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction\
KMS Misura et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of superbinding peptides
U Wiedemann et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
AV Morozov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Predicting specificity in bZIP coiled-coil protein interactions
JH Fong et al.
GENOME BIOLOGY (2004)
Optimization of specificity in a cellular protein interaction network by negative selection
A Zarrinpar et al.
NATURE (2003)
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
RM Levy et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Comprehensive identification of human bZIP interactions with coiled-coil arrays
JRS Newman et al.
SCIENCE (2003)
Activation of CD4 T cells by Raf-independent effectors of Ras
J Czyzyk et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Origins of PDZ domain ligand specificity - Structure determination and mutagenesis of the erbin PDZ domain
NJ Skelton et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library
MJ Feldhaus et al.
NATURE BIOTECHNOLOGY (2003)
Novel mode of ligand recognition by the Erbin PDZ domain
G Birrane et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
Automated design of specificity in molecular recognition
JJ Havranek et al.
NATURE STRUCTURAL BIOLOGY (2003)
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
HY Zhou et al.
PROTEIN SCIENCE (2002)
Combining computational and experimental screening for rapid optimization of protein properties
RJ Hayes et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
L Lu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
Designing gene libraries from protein profiles for combinatorial protein experiments
W Wang et al.
NUCLEIC ACIDS RESEARCH (2002)
Rotamer libraries in the 21st century
RL Dunbrack
CURRENT OPINION IN STRUCTURAL BIOLOGY (2002)
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
R Guerois et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Fast and Accurate Side-Chain Topology and Energy Refinement (FASTER) as a new method for protein structure optimization
J Desmet et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2002)
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
CW Carter et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
A comprehensive two-hybrid analysis to explore the yeast protein interactome
T Ito et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Computational method to reduce the search space for directed protein evolution
CA Voigt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure
H Kono et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
CA Voigt et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Structural basis for specificity switching of the Src SH2 domain
MS Kimber et al.
MOLECULAR CELL (2000)
分享论文
