SYNBIP: synthetic binding proteins for research, diagnosis and therapy

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

(2021) Paul-Albert Koenig et al.   SCIENCE

Anticancer peptides prediction with deep representation learning features

(2021) Zhibin Lv et al.   BRIEFINGS IN BIOINFORMATICS

Structural insights into the inhibition of glycine reuptake

(2021) Azadeh Shahsavar et al.   NATURE

De novo design of modular and tunable protein biosensors

(2021) Alfredo Quijano-Rubio et al.   NATURE

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

(2021) Zhen Chen et al.   NUCLEIC ACIDS RESEARCH

IsAb: a computational protocol for antibody design

(2021) Tianjian Liang et al.   BRIEFINGS IN BIOINFORMATICS

Computational design and modeling of nanobodies toward SARS‐CoV‐2 receptorbinding domain

(2021) Jingyi Yang et al.   Chemical Biology & Drug Design

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

Protein design and variant prediction using autoregressive generative models

(2021) Jung-Eun Shin et al.   Nature Communications

Data-driven computational protein design

(2021) Vincent Frappier et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Advances in machine learning for directed evolution

(2021) Bruce J Wittmann et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Engineered Protein Scaffolds as Next-Generation Therapeutics

(2020) Michaela Gebauer et al.   Annual Review of Pharmacology and Toxicology

Predicting Thermophilic Proteins by Machine Learning

(2020) Xian-Fang Wang et al.   Current Bioinformatics

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-guided discovery of a single-domain antibody agonist against human apelin receptor

(2020) Yanbin Ma et al.   Science Advances

Rosetta and the journey to predict proteins’ structures, 20 years on

(2020) Jad Abbass et al.   Current Bioinformatics

Monobodies as enabling tools for structural and mechanistic biology

(2020) Oliver Hantschel et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Generation of synthetic nanobodies against delicate proteins

(2020) Iwan Zimmermann et al.   Nature Protocols

State-of-the-art web services for de novo protein structure prediction

(2020) Luciano A Abriata et al.   BRIEFINGS IN BIOINFORMATICS

Synthetic nanobodies as angiotensin receptor blockers

(2020) Conor McMahon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Binding Characterization of GPCRs-Modulator by Molecular Complex Characterizing System (MCCS)

(2020) Zhiwei Feng et al.   ACS Chemical Neuroscience

MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs

(2020) Zhiwei Feng et al.   BRIEFINGS IN BIOINFORMATICS

Recent advances in the scaffold engineering of protein binders

(2020) Mohammad Karimi Baba Ahmadi et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

A phage‐displayed single‐chain Fab library optimized for rapid production of single‐chain IgGs

(2020) Rachel Hanna et al.   PROTEIN SCIENCE

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

(2020) Longxing Cao et al.   SCIENCE

Exploring the sequence fitness landscape of a bridge between protein folds

(2020) Pengfei Tian et al.   PLoS Computational Biology

Identification of sub-Golgi protein localization by use of deep representation learning features

(2020) Zhibin Lv et al.   BIOINFORMATICS

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Applications of Nanobodies

(2020) Serge Muyldermans   Annual Review of Animal Biosciences

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

Llama-inspired antibody fragment approved for rare blood disorder

(2019) Cormac Sheridan   NATURE BIOTECHNOLOGY

Machine learning-assisted directed protein evolution with combinatorial libraries

(2019) Zachary Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

COMBINES-CID: An Efficient Method for De Novo Engineering of Highly Specific Chemically Induced Protein Dimerization Systems

(2019) Shoukai Kang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

ICD-11

(2019) The Lancet   LANCET

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Nanobody approval gives domain antibodies a boost

(2019) Chris Morrison   NATURE REVIEWS DRUG DISCOVERY

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

(2019) Fuyi Li et al.   BIOINFORMATICS

Advances in protein structure prediction and design

(2019) Brian Kuhlman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Thera-SAbDab: the Therapeutic Structural Antibody Database

(2019) Matthew I J Raybould et al.   NUCLEIC ACIDS RESEARCH

The ABCD database: a repository for chemically defined antibodies

(2019) Wanessa C Lima et al.   NUCLEIC ACIDS RESEARCH

Innovation by Evolution: Bringing New Chemistry to Life (Nobel Lecture)

(2019) Frances H. Arnold   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein Secondary Structure Prediction: A Review of Progress and Directions

(2019) Tomasz Smolarczyk et al.   Current Bioinformatics

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

10-Year Update on Study Results Submitted to ClinicalTrials.gov

(2019) Deborah A. Zarin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Database resources of the National Center for Biotechnology Information

(2019) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Relevance of Molecular Docking Studies in Drug Designing

(2019) Ritu Jakhar et al.   Current Bioinformatics

Engineering of binding functions into proteins

(2019) Michaela Gebauer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Co-Evolutionary Fitness Landscapes for Sequence Design

(2018) Pengfei Tian et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Anticalin® Proteins as Therapeutic Agents in Human Diseases

(2018) Christine Rothe et al.   BIODRUGS

Indole Alkaloids as New Leads for the Design and Development of Novel DPP-IV Inhibitors for the Treatment of Diabetes

(2018) Kannan Narayanan Dhiraviam et al.   Current Bioinformatics

Engineered protein scaffolds as leads for synthetic inhibitors of protein–protein interactions

(2018) Michael G Wuo et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computational redesign of enzymes for regio- and enantioselective hydroamination

(2018) Ruifeng Li et al.   Nature Chemical Biology

Speed up to find the right ones: rapid discovery of functional nanobodies

(2018) Ulrich Rothbauer   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Yeast surface display platform for rapid discovery of conformationally selective nanobodies

(2018) Conor McMahon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Speed up to find the right ones: rapid discovery of functional nanobodies

(2018) Ulrich Rothbauer   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Yeast surface display platform for rapid discovery of conformationally selective nanobodies

(2018) Conor McMahon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ICD-11: in praise of good data

(2018) The Lancet Infectious Diseases   LANCET INFECTIOUS DISEASES

Compliance with requirement to report results on the EU Clinical Trials Register: cohort study and web resource

(2018) Ben Goldacre et al.   BMJ-British Medical Journal

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Folding pathway of an Ig domain is conserved on and off the ribosome

(2018) Pengfei Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

sdAb-DB: The Single Domain Antibody Database

(2018) Emily E. Wilton et al.   ACS Synthetic Biology

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Faster, deeper, smaller—the rise of antibody-like scaffolds

(2017) Brian Owens   NATURE BIOTECHNOLOGY

Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor–neutralizing therapy in patients with inflammatory bowel disease

(2017) Nathaniel R West et al.   NATURE MEDICINE

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

The DifferentialNet database of differential protein–protein interactions in human tissues

(2017) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

Monobodies and other synthetic binding proteins for expanding protein science

(2017) Fern Sha et al.   PROTEIN SCIENCE

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Targeting “Undruggable” Proteins: Design of Synthetic Cyclopeptides

(2016) Anna Russo et al.   CURRENT MEDICINAL CHEMISTRY

i-bodies, Human Single Domain Antibodies That Antagonize Chemokine Receptor CXCR4

(2016) Katherine Griffiths et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Inhibition of RAS function through targeting an allosteric regulatory site

(2016) Russell Spencer-Smith et al.   Nature Chemical Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Keratin mediates the recognition of apoptotic and necrotic cells through dendritic cell receptor DEC205/CD205

(2016) Longxing Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein engineering by highly parallel screening of computationally designed variants

(2016) M. G. F. Sun et al.   Science Advances

Designed Ankyrin Repeat Proteins (DARPins): Binding Proteins for Research, Diagnostics, and Therapy

(2015) Andreas Plückthun   Annual Review of Pharmacology and Toxicology

Protein binder woes

(2015)   NATURE METHODS

pH-dependent recognition of apoptotic and necrotic cells by the human dendritic cell receptor DEC205

(2015) Longxing Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling

(2015) Lora Mak et al.   Journal of Cheminformatics

Shark variable new antigen receptor biologics – a novel technology platform for therapeutic drug development

(2014) Marina Kovaleva et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

PyIgClassify: a database of antibody CDR structural classifications

(2014) Jared Adolf-Bryfogle et al.   NUCLEIC ACIDS RESEARCH

Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody

(2013) Aaron M. Ring et al.   NATURE

Recombinant Probes for Visualizing Endogenous Synaptic Proteins in Living Neurons

(2013) Garrett G. Gross et al.   NEURON

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

Structural insights for engineering binding proteins based on non-antibody scaffolds

(2012) Ryan N Gilbreth et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

(2012) S.-C. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-immunoglobulin based protein scaffolds

(2011) John Löfblom et al.   CURRENT OPINION IN BIOTECHNOLOGY

Molecular Design and Optimization of 99mTc-Labeled Recombinant Affibody Molecules Improves Their Biodistribution and Imaging Properties

(2011) H. Wallberg et al.   JOURNAL OF NUCLEAR MEDICINE

Designed ankyrin repeat proteins: a novel tool for testing epidermal growth factor receptor 2 expression in breast cancer

(2010) Jean-Philippe Theurillat et al.   MODERN PATHOLOGY

Ecallantide

(2010) Bruce Zuraw et al.   NATURE REVIEWS DRUG DISCOVERY

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Display scaffolds: protein engineering for novel therapeutics

(2008) S NUTTALL et al.   CURRENT OPINION IN PHARMACOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH