Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein

Structural biology data archiving - where we are and what lies ahead

(2018) Gerard J. Kleywegt et al.   FEBS LETTERS

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction

(2018) Chao Fang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction

(2018) Balachandran Manavalan et al.   Frontiers in Immunology

FledFold: A Novel Software for RNA Secondary Structure Prediction

(2017) Qi Zhao et al.   LETTERS IN ORGANIC CHEMISTRY

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models

(2017) Ali H. A. Maghrabi et al.   NUCLEIC ACIDS RESEARCH

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

(2017) Jieming Shi et al.   PLoS One

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

(2017) Jasmine Y. Young et al.   STRUCTURE

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

(2016) Marcin Magnus et al.   NUCLEIC ACIDS RESEARCH

Synthetic B-Cell Epitopes Eliciting Cross-Neutralizing Antibodies: Strategies for Future Dengue Vaccine

(2016) Babu Ramanathan et al.   PLoS One

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design

(2014) Ju Xin Chin et al.   BIOINFORMATICS

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

AllerTOP v.2—a server for in silico prediction of allergens

(2014) Ivan Dimitrov et al.   JOURNAL OF MOLECULAR MODELING

A novel multi-epitope peptide vaccine against cancer: An in silico approach

(2014) Navid Nezafat et al.   JOURNAL OF THEORETICAL BIOLOGY

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

Synthetic biology in mammalian cells: next generation research tools and therapeutics

(2014) Florian Lienert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

(2014) Xiaojun Xu et al.   PLoS One

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

(2013) Pingping Sun et al.   Computational and Mathematical Methods in Medicine

Dynamical Non-Equilibrium Molecular Dynamics

(2013) Giovanni Ciccotti et al.   Entropy

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

(2013) Tomasz Puton et al.   NUCLEIC ACIDS RESEARCH

T-cell epitope vaccine design by immunoinformatics

(2013) A. Patronov et al.   Open Biology

Fusion protein linkers: Property, design and functionality

(2012) Xiaoying Chen et al.   ADVANCED DRUG DELIVERY REVIEWS

Pharmacokinetics of recombinant bifunctional fusion proteins

(2012) Xiaoying Chen et al.   Expert Opinion on Drug Metabolism & Toxicology

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

(2012) J. P. G. L. M. Rodrigues et al.   NUCLEIC ACIDS RESEARCH

GalaxyWEB server for protein structure prediction and refinement

(2012) J. Ko et al.   NUCLEIC ACIDS RESEARCH

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

The MEMPACK alpha-helical transmembrane protein structure prediction server

(2011) T. Nugent et al.   BIOINFORMATICS

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

(2011) Dong Xu et al.   BIOPHYSICAL JOURNAL

A multiple-template approach to protein threading

(2011) Jian Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

(2010) F. Jossinet et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective

(2010) Nicolas Guex et al.   ELECTROPHORESIS

Immunoinformatics: an integrated scenario

(2010) Namrata Tomar et al.   IMMUNOLOGY

Major histocompatibility complex class I binding predictions as a tool in epitope discovery

(2010) Claus Lundegaard et al.   IMMUNOLOGY

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations

(2010) F. F. Gonzalez-Galarza et al.   NUCLEIC ACIDS RESEARCH

(PS)2-v2: template-based protein structure prediction server

(2009) Chih-Chieh Chen et al.   BMC BIOINFORMATICS

Impact of linker strain and flexibility in the design of a fragment-based inhibitor

(2009) Suhman Chung et al.   Nature Chemical Biology

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

QMEAN server for protein model quality estimation

(2009) Pascal Benkert et al.   NUCLEIC ACIDS RESEARCH

TOPCONS: consensus prediction of membrane protein topology

(2009) A. Bernsel et al.   NUCLEIC ACIDS RESEARCH

The Immune Epitope Database 2.0

(2009) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

ElliPro: a new structure-based tool for the prediction of antibody epitopes

(2008) Julia Ponomarenko et al.   BMC BIOINFORMATICS

Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research

(2008) Hong Lin et al.   BMC IMMUNOLOGY

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries

(2008) Yinghao Wu et al.   JOURNAL OF MOLECULAR BIOLOGY

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

(2008) David J Lynn et al.   Molecular Systems Biology

EpiToolKit—a web server for computational immunomics

(2008) Magdalena Feldhahn et al.   NUCLEIC ACIDS RESEARCH

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH

COBEpro: a novel system for predicting continuous B-cell epitopes

(2008) Michael J. Sweredoski et al.   PROTEIN ENGINEERING DESIGN & SELECTION

An introduction to epitope prediction methods and software

(2008) Xingdong Yang et al.   REVIEWS IN MEDICAL VIROLOGY

Enhanced Membrane Protein Topology Prediction Using a Hierarchical Classification Method and a New Scoring Function

(2007) Allan Lo et al.   JOURNAL OF PROTEOME RESEARCH

Benchmarking B cell epitope prediction: Underperformance of existing methods

(2004) Martin J. Blythe et al.   PROTEIN SCIENCE