DaReUS-Loop: a web server to model multiple loops in homology models

NGL viewer: web-based molecular graphics for large complexes

(2018) Alexander S Rose et al.   BIOINFORMATICS

DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins

(2018) Yasaman Karami et al.   Scientific Reports

PIGSPro: prediction of immunoGlobulin structures v2

(2017) Rosalba Lepore et al.   NUCLEIC ACIDS RESEARCH

Fast de novo discovery of low-energy protein loop conformations

(2017) Samuel W. K. Wong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational protein structure refinement: almost there, yet still so far to go

(2017) Michael Feig   Wiley Interdisciplinary Reviews-Computational Molecular Science

RCD+: Fast loop modeling server

(2016) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

SL2: an interactive webtool for modeling of missing segments in proteins

(2016) Jochen Ismer et al.   NUCLEIC ACIDS RESEARCH

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

Conformational sampling and structure prediction of multiple interacting loops in soluble andβ-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method

(2015) Ke Tang et al.   BIOINFORMATICS

Effective protein model structure refinement by loop modeling and overall relaxation

(2015) Gyu Rie Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies

(2014) K. Yamashita et al.   BIOINFORMATICS

Open Innovation Drug Discovery (OIDD): A Potential Path to Novel Therapeutic Chemical Space

(2014) Maria Alvim-Gaston et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

(2014) Hahnbeom Park et al.   PLoS One

Low-resolution structural modeling of protein interactome

(2013) Ilya A Vakser   CURRENT OPINION IN STRUCTURAL BIOLOGY

Template-based structure modeling of protein–protein interactions

(2013) Andras Szilagyi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins

(2013) Daniel Holtby et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains

(2013) Shide Liang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Loop prediction for a GPCR homology model: Algorithms and results

(2013) Dahlia A. Goldfeld et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Loop Modeling with Optimized Backbone Potential Functions

(2012) Shide Liang et al.   Journal of Chemical Theory and Computation

Spatial clustering of protein binding sites for template based protein docking

(2011) Anisah W. Ghoorah et al.   BIOINFORMATICS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The FALC-Loop web server for protein loop modeling

(2011) J. Ko et al.   NUCLEIC ACIDS RESEARCH

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

(2009) P. W. Hildebrand et al.   NUCLEIC ACIDS RESEARCH

RosettaAntibody: antibody variable region homology modeling server

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