The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

Accelerated Estimation of Long-timescale Kinetics by Combining Weighted Ensemble Simulation with Markov Model “Microstates” using Non-Markovian Theory

(2020) Jeremy T. Copperman et al.   BIOPHYSICAL JOURNAL

Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019‐nCoV

(2020) Jared S. Morse et al.   CHEMBIOCHEM

α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment

(2020) Linlin Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure-based stabilization of non-native protein-protein interactions of coronavirus nucleocapsid proteins in antiviral drug design

(2020) Shan-Meng Lin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure–Activity Relationship Studies on Diversified Salicylamide Derivatives as Potent Inhibitors of Human Adenovirus Infection

(2020) Jimin Xu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Coronavirus puts drug repurposing on the fast track

(2020) Charlotte Harrison   NATURE BIOTECHNOLOGY

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

Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans

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

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies

(2020) Syed Faraz Ahmed et al.   Viruses-Basel

ProtCID: a data resource for structural information on protein interactions

(2020) Qifang Xu et al.   Nature Communications

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

(2020) Jasper Fuk-Woo Chan et al.   Emerging Microbes & Infections

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms

(2020) Bodee Nutho et al.   BIOCHEMISTRY

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence

(2020) Mayya Sedova et al.   BIOINFORMATICS

Potent antiviral activity of novel multi-substituted 4-anilinoquin(az)olines

(2020) Sirle Saul et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structural basis for RNA replication by the SARS-CoV-2 polymerase

(2020) Quan Wang et al.   CELL

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

(2020) Qihui Wang et al.   CELL

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

(2020) Shuai Xia et al.   CELL RESEARCH

Drug Development and Medicinal Chemistry Efforts toward SARS‐Coronavirus and Covid‐19 Therapeutics

(2020) Arun K. Ghosh et al.   ChemMedChem

Dose Rationale for Favipiravir Use in Patients Infected With SARS‐CoV‐2

(2020) Philippine Eloy et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Boosting the arsenal against COVID-19 through computational drug repurposing

(2020) Gennaro Ciliberto et al.   DRUG DISCOVERY TODAY

Ligand‐centered assessment of SARS‐CoV‐2 drug target models in the Protein Data Bank

(2020) Alexander Wlodawer et al.   FEBS Journal

Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds

(2020) André Fischer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atoms Simulations

(2020) Angelo Spinello et al.   Journal of Physical Chemistry Letters

Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial

(2020) Yeming Wang et al.   LANCET

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

(2020) Dora Pinto et al.   NATURE

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

(2020) Zhenming Jin et al.   NATURE

How to Discover Antiviral Drugs Quickly

(2020) Jerry M. Parks et al.   NEW ENGLAND JOURNAL OF MEDICINE

Site-specific glycan analysis of the SARS-CoV-2 spike

(2020) Yasunori Watanabe et al.   SCIENCE

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease

(2020) Wenhao Dai et al.   SCIENCE

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir

(2020) Wanchao Yin et al.   SCIENCE

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

Evaluation of the efficacy and safety of intravenous remdesivir in adult patients with severe COVID-19: study protocol for a phase 3 randomized, double-blind, placebo-controlled, multicentre trial

(2020) Yeming Wang et al.   Trials

Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins

(2020) Suhas Srinivasan et al.   Viruses-Basel

Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV

(2020) Xiuyuan Ou et al.   Nature Communications

Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites

(2020) Sisi Kang et al.   Acta Pharmaceutica Sinica B

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

(2020) Qianqian Li et al.   CELL

A Universal Design of Betacoronavirus Vaccines against COVID-19, MERS, and SARS

(2020) Lianpan Dai et al.   CELL

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

(2020) Christopher O. Barnes et al.   CELL

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease

(2020) Chunlong Ma et al.   CELL RESEARCH

Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics

(2020) Sajjad Ahmad et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

(2020) Silvia Gervasoni et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics

(2020) Ruchir Gupta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)

(2020) Ryo Hatada et al.   Journal of Chemical Information and Modeling

Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease

(2020) Anuj Gahlawat et al.   Journal of Chemical Information and Modeling

Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein‐enhanced fitness in SARS‐COV ‐2

(2020) I. Olaposi Omotuyi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

COVID-19: Drug Targets and Potential Treatments

(2020) Carmen Gil et al.   JOURNAL OF MEDICINAL CHEMISTRY

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

(2020) Hyeonuk Woo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence

(2020) Naveen Vankadari   Journal of Physical Chemistry Letters

The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach

(2020) Luisa Di Paola et al.   JOURNAL OF PROTEOME RESEARCH

Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study

(2020) Abdo A. Elfiky   LIFE SCIENCES

Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids

(2020) Gerard Kian-Meng Goh et al.   MICROBIAL PATHOGENESIS

Potently neutralizing and protective human antibodies against SARS-CoV-2

(2020) Seth J. Zost et al.   NATURE

Repurposing the mucolytic cough suppressant and TMPRSS2 protease inhibitor bromhexine for the prevention and management of SARS-CoV-2 infection

(2020) Roberto Maggio et al.   PHARMACOLOGICAL RESEARCH

Possible use of the mucolytic drug, bromhexine hydrochloride, as a prophylactic agent against SARS-CoV-2 infection based on its action on the Transmembrane Serine Protease 2

(2020) Solomon Habtemariam et al.   PHARMACOLOGICAL RESEARCH

Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2

(2020) Yuan-Lin Kang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

(2020) Alina Baum et al.   SCIENCE

Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2

(2020) Kui K. Chan et al.   SCIENCE

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes

(2020) Ching-Lin Hsieh et al.   SCIENCE

Structure of the Pandemic

(2020) Sarah Kearns   STRUCTURE

Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates

(2020) Ryunosuke Yoshino et al.   Scientific Reports

A candidate multi-epitope vaccine against SARS-CoV-2

(2020) Tamalika Kar et al.   Scientific Reports

Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review

(2020) Gi Uk Jeong et al.   Frontiers in Microbiology

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences

(2020) Yue Xing et al.   Frontiers in Microbiology

Structure-based drug designing and immunoinformatics approach for SARS-CoV-2

(2020) Pritam Kumar Panda et al.   Science Advances

Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets

(2020) Sumit Mukherjee et al.   Vaccines

Structure-based virtual screening of phytochemicals and repurposing of FDA approved antiviral drugs unravels lead molecules as potential inhibitors of coronavirus 3C-like protease enzyme

(2020) Arun Bahadur Gurung et al.   JOURNAL OF KING SAUD UNIVERSITY SCIENCE

Current Status of COVID-19 Therapies and Drug Repositioning Applications

(2020) Ozlem Altay et al.   iScience

Allosteric Inhibition of the SARS‐CoV‐2 Main Protease: Insights from Mass Spectrometry Based Assays

(2020) Tarick J. El‐Baba et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

(2020) Jiandong Huo et al.   Cell Host & Microbe

COVID‐19 drug repurposing: A review of computational screening methods, clinical trials, and protein interaction assays

(2020) Xueqing Wang et al.   MEDICINAL RESEARCH REVIEWS

Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

(2020) Stephanie Portelli et al.   NATURE GENETICS

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

(2020) Joana Damas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

(2020) Beata Turoňová et al.   SCIENCE

Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity

(2020) Ariel Fernández   ACS Medicinal Chemistry Letters

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

(2020) Alice Douangamath et al.   Nature Communications

Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication

(2020) Wayne Vuong et al.   Nature Communications

SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals

(2020) S. D. Lam et al.   Scientific Reports

Heterogeneous antibodies against SARS-CoV-2 spike receptor binding domain and nucleocapsid with implications for COVID-19 immunity

(2020) Kathleen M. McAndrews et al.   JCI Insight

The SIRAH 2.0 Force Field: Altius, Fortius, Citius

(2019) Matías R. Machado et al.   Journal of Chemical Theory and Computation

AlphaFold at CASP13

(2019) Mohammed AlQuraishi   BIOINFORMATICS

SeRenDIP: SEquential REmasteriNg to DerIve Profiles for fast and accurate predictions of PPI interface positions

(2019) Qingzhen Hou et al.   BIOINFORMATICS

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

(2019) Carlos H M Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis

(2019) Zhihui Jia et al.   NUCLEIC ACIDS RESEARCH

Structural mechanisms of phospholipid activation of the human TPC2 channel

(2019) Ji She et al.   eLife

Deep‐learning contact‐map guided protein structure prediction in CASP13

(2019) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Design, Synthesis, and Biological Evaluation of Substituted 4,6-Dihydrospiro[[1,2,3]triazolo[4,5-b]pyridine-7,3′-indoline]-2′,5(3H)-dione Analogues as Potent NS4B Inhibitors for the Treatment of Dengue Virus Infection

(2019) Jimin Xu et al.   JOURNAL OF MEDICINAL CHEMISTRY

QMEANDisCo – Distance Constraints Applied on Model Quality Estimation

(2019) Gabriel Studer et al.   BIOINFORMATICS

PDBe-KB: a community-driven resource for structural and functional annotations

(2019) et al.   NUCLEIC ACIDS RESEARCH

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

(2019) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors

(2019) Geraldo Rodrigues Sartori et al.   PLoS One

X-ray Structures of the Proprotein Convertase Furin Bound with Substrate Analogue Inhibitors Reveal Substrate Specificity Determinants beyond the S4 Pocket

(2018) Sven O. Dahms et al.   BIOCHEMISTRY

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

(2018) Birgit H M Meldal et al.   NUCLEIC ACIDS RESEARCH

CATH: expanding the horizons of structure-based functional annotations for genome sequences

(2018) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

(2018) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

(2018) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

(2018) John D. Westbrook et al.   STRUCTURE

Anticancer kinase inhibitors impair intracellular viral trafficking and exert broad-spectrum antiviral effects

(2017) Elena Bekerman et al.   JOURNAL OF CLINICAL INVESTIGATION

Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections

(2017) Sherine E. Thomas et al.   JOURNAL OF MOLECULAR BIOLOGY

Neurovirulent Murine Coronavirus JHM.SD Uses Cellular Zinc Metalloproteases for Virus Entry and Cell-Cell Fusion

(2017) Judith M. Phillips et al.   JOURNAL OF VIROLOGY

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

(2017) António J M Ribeiro et al.   NUCLEIC ACIDS RESEARCH

MetalPDB in 2018: a database of metal sites in biological macromolecular structures

(2017) Valeria Putignano et al.   NUCLEIC ACIDS RESEARCH

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

(2016) M. Madan Babu   BIOCHEMICAL SOCIETY TRANSACTIONS

Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity

(2016) Rita Pancsa et al.   BIOPHYSICAL JOURNAL

An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy

(2016) Thanigaimalai Pillaiyar et al.   JOURNAL OF MEDICINAL CHEMISTRY

EMPIAR: a public archive for raw electron microscopy image data

(2016) Andrii Iudin et al.   NATURE METHODS

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

(2016) Alexandra C Walls et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The SWISS-MODEL Repository—new features and functionality

(2016) Stefan Bienert et al.   NUCLEIC ACIDS RESEARCH

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

(2016) Akira R. Kinjo et al.   NUCLEIC ACIDS RESEARCH

The Conserved Coronavirus Macrodomain Promotes Virulence and Suppresses the Innate Immune Response during Severe Acute Respiratory Syndrome Coronavirus Infection

(2016) Anthony R. Fehr et al.   mBio

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

(2016) Alexandra C Walls et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protease inhibitors targeting coronavirus and filovirus entry

(2015) Yanchen Zhou et al.   ANTIVIRAL RESEARCH

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

ProKinO: A Unified Resource for Mining the Cancer Kinome

(2015) Daniel Ian McSkimming et al.   HUMAN MUTATION

Aquaria: simplifying discovery and insight from protein structures

(2015) Seán I O'Donoghue et al.   NATURE METHODS

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Two-pore channels control Ebola virus host cell entry and are drug targets for disease treatment

(2015) Yasuteru Sakurai et al.   SCIENCE

AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble

(2014) Badi’ Abdul-Wahid et al.   Journal of Chemical Information and Modeling

Structural Basis for the Identification of the N-Terminal Domain of Coronavirus Nucleocapsid Protein as an Antiviral Target

(2014) Shing-Yen Lin et al.   JOURNAL OF MEDICINAL CHEMISTRY

PredictProtein—an open resource for online prediction of protein structural and functional features

(2014) Guy Yachdav et al.   NUCLEIC ACIDS RESEARCH

The DynaMine webserver: predicting protein dynamics from sequence

(2014) Elisa Cilia et al.   NUCLEIC ACIDS RESEARCH

OMICtools: an informative directory for multi-omic data analysis

(2014) V. J. Henry et al.   Database-The Journal of Biological Databases and Curation

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

Optimization of Triazine Nitriles as Rhodesain Inhibitors: Structure-Activity Relationships, Bioisosteric Imidazopyridine Nitriles, and X-ray Crystal Structure Analysis with Human Cathepsin L

(2013) Veronika Ehmke et al.   ChemMedChem

SCOP2 prototype: a new approach to protein structure mining

(2013) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

From protein sequence to dynamics and disorder with DynaMine

(2013) Elisa Cilia et al.   Nature Communications

RNA synthetic mechanisms employed by diverse families of RNA viruses

(2013) Sarah M. McDonald   Wiley Interdisciplinary Reviews-RNA

Halogen Bonding at the Active Sites of Human Cathepsin L and MEK1 Kinase: Efficient Interactions in Different Environments

(2011) Leo A. Hardegger et al.   ChemMedChem

Unstructural biology coming of age

(2011) Peter Tompa   CURRENT OPINION IN STRUCTURAL BIOLOGY

2,6-Bis-arylmethyloxy-5-hydroxychromones with antiviral activity against both hepatitis C virus (HCV) and SARS-associated coronavirus (SCV)

(2011) Mi Kyoung Kim et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Toward the estimation of the absolute quality of individual protein structure models

(2010) Pascal Benkert et al.   BIOINFORMATICS

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Aryl diketoacids (ADK) selectively inhibit duplex DNA-unwinding activity of SARS coronavirus NTPase/helicase

(2009) Chaewoon Lee et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

PIKfyve Regulation of Endosome-Linked Pathways

(2009) Jane de Lartigue et al.   TRAFFIC

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules

(2008) Eran Hodis et al.   GENOME BIOLOGY