- Home
- Publications
- Publication Search
- Publication Details
Title
Advances in protein structure prediction and design
Authors
Keywords
-
Journal
NATURE REVIEWS MOLECULAR CELL BIOLOGY
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-08-16
DOI
10.1038/s41580-019-0163-x
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- De novo design of potent and selective mimics of IL-2 and IL-15
- (2019) Daniel-Adriano Silva et al. NATURE
- Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1
- (2019) Vincent Frappier et al. STRUCTURE
- Packing of apolar side chains enables accurate design of highly stable membrane proteins
- (2019) Marco Mravic et al. SCIENCE
- Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus
- (2019) Jessica Marcandalli et al. CELL
- Computational design of structured loops for new protein functions
- (2019) Kale Kundert et al. BIOLOGICAL CHEMISTRY
- A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold
- (2019) Yuxi Liu et al. Nature Communications
- Principles of Protein Stability and Their Application in Computational Design
- (2018) Adi Goldenzweig et al. Annual Review of Biochemistry
- High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
- (2018) David T Jones et al. BIOINFORMATICS
- Computational protein design — the next generation tool to expand synthetic biology applications
- (2018) Pablo Gainza-Cirauqui et al. CURRENT OPINION IN BIOTECHNOLOGY
- Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program
- (2018) Sharon L. Guffy et al. Journal of Chemical Information and Modeling
- Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design
- (2018) Jack B. Maguire et al. Journal of Chemical Theory and Computation
- SWISS-MODEL: homology modelling of protein structures and complexes
- (2018) Andrew Waterhouse et al. NUCLEIC ACIDS RESEARCH
- Bispecific antibodies for cancer therapy: A review
- (2018) Anuradha Krishnamurthy et al. PHARMACOLOGY & THERAPEUTICS
- Protein homology model refinement by large-scale energy optimization
- (2018) Hahnbeom Park et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system
- (2018) Yuxi Liu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Accurate computational design of multipass transmembrane proteins
- (2018) Peilong Lu et al. SCIENCE
- Highly active enzymes by automated combinatorial backbone assembly and sequence design
- (2018) Gideon Lapidoth et al. Nature Communications
- RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
- (2018) Jared Adolf-Bryfogle et al. PLoS Computational Biology
- Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks
- (2018) Yang Liu et al. Cell Systems
- De novo design of a fluorescence-activating β-barrel
- (2018) Jiayi Dou et al. NATURE
- Computational design of chemogenetic and optogenetic split proteins
- (2018) Onur Dagliyan et al. Nature Communications
- Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides
- (2018) Yu Tian et al. BIOMACROMOLECULES
- OSPREY 3.0: Open-source protein redesign for you, with powerful new features
- (2018) Mark A. Hallen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Programmable design of orthogonal protein heterodimers
- (2018) Zibo Chen et al. NATURE
- De novo design of a non-local β-sheet protein with high stability and accuracy
- (2018) Enrique Marcos et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Experimental accuracy in protein structure refinement via molecular dynamics simulations
- (2018) Lim Heo et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- De novo design of self-assembling helical protein filaments
- (2018) Hao Shen et al. SCIENCE
- The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
- (2017) Rebecca F. Alford et al. Journal of Chemical Theory and Computation
- Computational protein design: a review
- (2017) Ivan Coluzza JOURNAL OF PHYSICS-CONDENSED MATTER
- Computational Design of a Photocontrolled Cytosine Deaminase
- (2017) Kristin M. Blacklock et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Massively parallel de novo protein design for targeted therapeutics
- (2017) Aaron Chevalier et al. NATURE
- Evolution of a designed protein assembly encapsulating its own RNA genome
- (2017) Gabriel L. Butterfield et al. NATURE
- Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo
- (2017) Ajasja Ljubetič et al. NATURE BIOTECHNOLOGY
- Rational design of proteins that exchange on functional timescales
- (2017) James A Davey et al. Nature Chemical Biology
- De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy
- (2017) Nicholas F. Polizzi et al. Nature Chemistry
- Principles for computational design of binding antibodies
- (2017) Dror Baran et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen
- (2017) Ivan Campeotto et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies
- (2017) K. J. Froning et al. PROTEIN SCIENCE
- Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12
- (2017) Chengxin Zhang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Principles for designing proteins with cavities formed by curved β sheets
- (2017) Enrique Marcos et al. SCIENCE
- Global analysis of protein folding using massively parallel design, synthesis, and testing
- (2017) Gabriel J. Rocklin et al. SCIENCE
- Protein structure determination using metagenome sequence data
- (2017) Sergey Ovchinnikov et al. SCIENCE
- Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
- (2017) Sheng Wang et al. PLoS Computational Biology
- Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1
- (2017) Justin M Jenson et al. eLife
- Computational design of environmental sensors for the potent opioid fentanyl
- (2017) Matthew J Bick et al. eLife
- Structured States of Disordered Proteins from Genomic Sequences
- (2016) Agnes Toth-Petroczy et al. CELL
- Algorithms for protein design
- (2016) Pablo Gainza et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
- (2016) Hahnbeom Park et al. Journal of Chemical Theory and Computation
- Fast search algorithms for computational protein design
- (2016) Seydou Traoré et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability
- (2016) Adi Goldenzweig et al. MOLECULAR CELL
- The coming of age of de novo protein design
- (2016) Po-Ssu Huang et al. NATURE
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- IMG/M: integrated genome and metagenome comparative data analysis system
- (2016) I-Min A. Chen et al. NUCLEIC ACIDS RESEARCH
- Tertiary alphabet for the observable protein structural universe
- (2016) Craig O. Mackenzie et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Engineering extrinsic disorder to control protein activity in living cells
- (2016) Onur Dagliyan et al. SCIENCE
- De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
- (2016) S. E. Boyken et al. SCIENCE
- Design of structurally distinct proteins using strategies inspired by evolution
- (2016) T. M. Jacobs et al. SCIENCE
- Accurate design of megadalton-scale two-component icosahedral protein complexes
- (2016) J. B. Bale et al. SCIENCE
- Computationally Designed Bispecific Antibodies using Negative State Repertoires
- (2016) Andrew Leaver-Fay et al. STRUCTURE
- Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer
- (2016) Stephanie Berger et al. eLife
- Computationally designed peptides for self-assembly of nanostructured lattices
- (2016) H. V. Zhang et al. Science Advances
- Protein stability: computation, sequence statistics, and new experimental methods
- (2015) Thomas J Magliery CURRENT OPINION IN STRUCTURAL BIOLOGY
- De novo protein design: how do we expand into the universe of possible protein structures?
- (2015) Derek N Woolfson et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta
- (2015) Matthew J. O’Meara et al. Journal of Chemical Theory and Computation
- Rational design of α-helical tandem repeat proteins with closed architectures
- (2015) Lindsey Doyle et al. NATURE
- Exploring the repeat protein universe through computational protein design
- (2015) TJ Brunette et al. NATURE
- Deep learning
- (2015) Yann LeCun et al. NATURE
- De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
- (2015) Po-Ssu Huang et al. Nature Chemical Biology
- The I-TASSER Suite: protein structure and function prediction
- (2015) Jianyi Yang et al. NATURE METHODS
- Control over overall shape and size in de novo designed proteins
- (2015) Yu-Ru Lin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structural basis for nucleotide exchange in heterotrimeric G proteins
- (2015) R. O. Dror et al. SCIENCE
- Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces
- (2015) S. Gonen et al. SCIENCE
- Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
- (2015) Noah Ollikainen et al. PLoS Computational Biology
- FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
- (2015) David Bednar et al. PLoS Computational Biology
- Large-scale determination of previously unsolved protein structures using evolutionary information
- (2015) Sergey Ovchinnikov et al. eLife
- Protein design algorithms predict viable resistance to an experimental antifolate
- (2015) Stephanie M. Reeve et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
- (2014) David T. Jones et al. BIOINFORMATICS
- Proof of principle for epitope-focused vaccine design
- (2014) Bruno E. Correia et al. NATURE
- Accurate design of co-assembling multi-component protein nanomaterials
- (2014) Neil P. King et al. NATURE
- Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface
- (2014) Steven M Lewis et al. NATURE BIOTECHNOLOGY
- PyIgClassify: a database of antibody CDR structural classifications
- (2014) Jared Adolf-Bryfogle et al. NUCLEIC ACIDS RESEARCH
- Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins
- (2014) Gurkan Guntas et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational de novo design of a four-helix bundle protein-DND_4HB
- (2014) Grant S. Murphy et al. PROTEIN SCIENCE
- De novo design of a transmembrane Zn2+-transporting four-helix bundle
- (2014) Nathan H. Joh et al. SCIENCE
- Computational design of water-soluble α-helical barrels
- (2014) Andrew R. Thomson et al. SCIENCE
- High thermodynamic stability of parametrically designed helical bundles
- (2014) Po-Ssu Huang et al. SCIENCE
- Computational Enzyme Design
- (2013) Gert Kiss et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks
- (2013) Yang Shen et al. JOURNAL OF BIOMOLECULAR NMR
- Computational design of ligand-binding proteins with high affinity and selectivity
- (2013) Christine E. Tinberg et al. NATURE
- Reprogramming an ATP-driven protein machine into a light-gated nanocage
- (2013) Daniel Hoersch et al. Nature Nanotechnology
- High-Resolution Comparative Modeling with RosettaCM
- (2013) Yifan Song et al. STRUCTURE
- Protein folding and de novo protein design for biotechnological applications
- (2013) George A. Khoury et al. TRENDS IN BIOTECHNOLOGY
- Advances in structure-based vaccine design
- (2013) Daniel W Kulp et al. Current Opinion in Virology
- Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
- (2012) Thomas A. Hopf et al. CELL
- Principles for designing ideal protein structures
- (2012) Nobuyasu Koga et al. NATURE
- Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
- (2012) T. Nugent et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Automated selection of stabilizing mutations in designed and natural proteins
- (2012) B. Borgo et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
- (2012) G. T. Kapp et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds
- (2012) P. Benjamin Stranges et al. PROTEIN SCIENCE
- Computational identification of self-inhibitory peptides from envelope proteins
- (2012) Yongtao Xu et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
- (2012) N. P. King et al. SCIENCE
- Structure of a 16-nm Cage Designed by Using Protein Oligomers
- (2012) Y.-T. Lai et al. SCIENCE
- Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core
- (2012) Grant S. Murphy et al. STRUCTURE
- PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
- (2011) David T. Jones et al. BIOINFORMATICS
- SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
- (2011) Eshel Faraggi et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- (2011) Michael Remmert et al. NATURE METHODS
- A Generic Program for Multistate Protein Design
- (2011) Andrew Leaver-Fay et al. PLoS One
- Protein 3D Structure Computed from Evolutionary Sequence Variation
- (2011) Debora S. Marks et al. PLoS One
- Direct-coupling analysis of residue coevolution captures native contacts across many protein families
- (2011) F. Morcos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
- (2011) S. J. Fleishman et al. SCIENCE
- How Fast-Folding Proteins Fold
- (2011) K. Lindorff-Larsen et al. SCIENCE
- Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
- (2010) Gia G. Maisuradze et al. JOURNAL OF PHYSICAL CHEMISTRY A
- An exciting but challenging road ahead for computational enzyme design
- (2010) David Baker PROTEIN SCIENCE
- Learning generative models for protein fold families
- (2010) Sivaraman Balakrishnan et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- SAM-T08, HMM-based protein structure prediction
- (2009) K. Karplus NUCLEIC ACIDS RESEARCH
- Improved prediction of protein side-chain conformations with SCWRL4
- (2009) Georgii G. Krivov et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- The Protein Folding Problem
- (2008) Ken A. Dill et al. Annual Review of Biophysics
- The MARTINI Coarse-Grained Force Field: Extension to Proteins
- (2008) Luca Monticelli et al. Journal of Chemical Theory and Computation
- Kemp elimination catalysts by computational enzyme design
- (2008) Daniela Röthlisberger et al. NATURE
- Identification of direct residue contacts in protein-protein interaction by message passing
- (2008) M. Weigt et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
- (2008) Lies Baeten et al. PLoS Computational Biology
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started