Macromolecular modeling and design in Rosetta: recent methods and frameworks

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures

(2020) Jianfu Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-state design of flexible proteins predicts sequences optimal for conformational change

(2020) Marion F. Sauer et al.   PLoS Computational Biology

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane

(2020) Rebecca F. Alford et al.   BIOPHYSICAL JOURNAL

Better together: Elements of successful scientific software development in a distributed collaborative community

(2020) Julia Koehler Leman et al.   PLoS Computational Biology

Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses

(2019) Alexander M. Sevy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid determination of quaternary protein structures in complex biological samples

(2019) Simon Hauri et al.   Nature Communications

Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta

(2019) Melanie L. Aprahamian et al.   Journal of Chemical Theory and Computation

BCL::Mol2D—a robust atom environment descriptor for QSAR modeling and lead optimization

(2019) Oanh Vu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind tests of RNA–protein binding affinity prediction

(2019) Kalli Kappel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes

(2019) Shourya S. Roy Burman et al.   STRUCTURE

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

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

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation

(2019) Alexander S. Ford et al.   PROTEIN SCIENCE

Analysis of distance‐based protein structure prediction by deep learning in CASP13

(2019) Jinbo Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints

(2019) Georg Kuenze et al.   STRUCTURE

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

(2019) Andrew W. Senior et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data

(2018) Melanie L. Aprahamian et al.   ANALYTICAL CHEMISTRY

Efficient flexible backbone protein–protein docking for challenging targets

(2018) Nicholas A Marze et al.   BIOINFORMATICS

A Benchmarking Study of Peptide–Biomineral Interactions

(2018) Michael S. Pacella et al.   CRYSTAL GROWTH & DESIGN

Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review

(2018) Darwin Y. Fu et al.   Journal of Chemical Information and Modeling

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

Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation

(2018) Kyle A. Barlow et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces

(2018) Joseph H. Lubin et al.   LANGMUIR

TCRmodel: high resolution modeling of T cell receptors from sequence

(2018) Ragul Gowthaman et al.   NUCLEIC ACIDS RESEARCH

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

A computational method for the design of nested proteins by loop-directed domain insertion

(2018) Kristin M. Blacklock et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra

(2018) Thomas Evangelidis et al.   Nature Communications

Highly active enzymes by automated combinatorial backbone assembly and sequence design

(2018) Gideon Lapidoth et al.   Nature Communications

Essentials of de novo protein design: Methods and applications

(2018) Enrique Marcos et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

(2018) Jared Adolf-Bryfogle et al.   PLoS Computational Biology

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

(2018) Jeliazko R. Jeliazkov et al.   Frontiers in Immunology

A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations

(2018) Jugmohit S. Toor et al.   Frontiers in Immunology

Blind prediction of noncanonical RNA structure at atomic accuracy

(2018) Andrew M. Watkins et al.   Science Advances

AbPredict 2: A server for accurate and unstrained structure prediction of antibody variable domains

(2018) Gideon Lapidoth et al.   BIOINFORMATICS

Fast design of arbitrary length loops in proteins using InteractiveRosetta

(2018) William F. Hooper et al.   BMC BIOINFORMATICS

Computational Design of Synthetic Enzymes

(2018) Valerie Vaissier Welborn et al.   CHEMICAL REVIEWS

Programmable design of orthogonal protein heterodimers

(2018) Zibo Chen et al.   NATURE

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

(2018) Kalli Kappel et al.   NATURE METHODS

De novo design of a non-local β-sheet protein with high stability and accuracy

(2018) Enrique Marcos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Automatically Fixing Errors in Glycoprotein Structures with Rosetta

(2018) Brandon Frenz et al.   STRUCTURE

Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking

(2018) Kalli Kappel et al.   STRUCTURE

Rosetta FunFolDes – A general framework for the computational design of functional proteins

(2018) Jaume Bonet et al.   PLoS Computational Biology

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps

(2017) Brandon Frenz et al.   NATURE METHODS

Modeling and docking of antibody structures with Rosetta

(2017) Brian D Weitzner et al.   Nature Protocols

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

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures

(2017) Bobo Dang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

(2017) Rocco Moretti et al.   PROTEIN SCIENCE

Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints

(2017) Katrin Reichel et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12

(2017) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Comprehensive computational design of ordered peptide macrocycles

(2017) Parisa Hosseinzadeh et al.   SCIENCE

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions

(2017) Jason K. Lai et al.   STRUCTURE

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

(2017) Nawsad Alam et al.   PLoS Computational Biology

MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory

(2017) Aliza B. Rubenstein et al.   PLoS Computational Biology

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

(2016) Brian J. Bender et al.   BIOCHEMISTRY

Documentation of an Imperative To Improve Methods for Predicting Membrane Protein Stability

(2016) Brett M. Kroncke et al.   BIOCHEMISTRY

Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein–Protein Interactions

(2016) David K. Johnson et al.   Journal of Chemical Information and Modeling

Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking

(2016) Anita K. Nivedha et al.   Journal of Chemical Theory and Computation

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

Residue-centric modeling and design of saccharide and glycoconjugate structures

(2016) Jason W. Labonte et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint

(2016) Brian D. Weitzner et al.   JOURNAL OF IMMUNOLOGY

Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins

(2016) Kala Bharath Pilla et al.   JOURNAL OF MOLECULAR BIOLOGY

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Accurate de novo design of hyperstable constrained peptides

(2016) Gaurav Bhardwaj et al.   NATURE

Peptiderive server: derive peptide inhibitors from protein–protein interactions

(2016) Yuval Sedan et al.   NUCLEIC ACIDS RESEARCH

The SWISS-MODEL Repository—new features and functionality

(2016) Stefan Bienert et al.   NUCLEIC ACIDS RESEARCH

The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70

(2016) Asmit Bhowmick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Improving Loop Modeling of the Antibody Complementarity-Determining Region 3 Using Knowledge-Based Restraints

(2016) Jessica A. Finn et al.   PLoS One

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

(2016) Dzmitry Padhorny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

(2016) Brandon J. DeKosky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind tests of RNA nearest-neighbor energy prediction

(2016) Fang-Chieh Chou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved prediction of antibody VL–VHorientation

(2016) Nicholas A. Marze et al.   PROTEIN ENGINEERING DESIGN & SELECTION

High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments

(2016) Christoffer H. Norn et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

(2016) Ray Yu-Ruei Wang et al.   eLife

High-resolution protein–protein docking by global optimization: recent advances and future challenges

(2015) Hahnbeom Park 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

Guaranteed Discrete Energy Optimization on Large Protein Design Problems

(2015) David Simoncini et al.   Journal of Chemical Theory and Computation

DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites

(2015) Ragul Gowthaman et al.   JOURNAL OF MEDICINAL CHEMISTRY

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

(2015) Frank DiMaio et al.   NATURE METHODS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

De novo protein structure determination from near-atomic-resolution cryo-EM maps

(2015) Ray Yu-Ruei Wang et al.   NATURE METHODS

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

(2015) Shane Ó Conchúir et al.   PLoS One

Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

(2015) Samuel DeLuca et al.   PLoS One

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

(2015) Gideon D. Lapidoth et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences

(2015) Alexander M. Sevy et al.   PLoS Computational Biology

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction

(2015) Tatjana Braun et al.   PLoS Computational Biology

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

(2015) Noah Ollikainen et al.   PLoS Computational Biology

An Integrated Framework Advancing Membrane Protein Modeling and Design

(2015) Rebecca F. Alford et al.   PLoS Computational Biology

Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations

(2015) David K. Johnson et al.   PLoS Computational Biology

DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites

(2015) Ragul Gowthaman et al.   PLoS One

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

Automatic NOESY assignment in CS-RASREC-Rosetta

(2014) Oliver F. Lange   JOURNAL OF BIOMOLECULAR NMR

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

(2014) Parin Sripakdeevong et al.   NATURE METHODS

Massively parallel determination and modeling of endonuclease substrate specificity

(2014) Summer B. Thyme et al.   NUCLEIC ACIDS RESEARCH

Removing T-cell epitopes with computational protein design

(2014) C. King et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

(2014) Brian D. Weitzner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational modeling of membrane proteins

(2014) Julia Koehler Leman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta

(2014) Paolo Rossi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved Docking of Polypeptides with Glide

(2013) Ivan Tubert-Brohman et al.   Journal of Chemical Information and Modeling

Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy

(2013) Jeremy H. Mills et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Improved low-resolution crystallographic refinement with Phenix and Rosetta

(2013) Frank DiMaio et al.   NATURE METHODS

Reprogramming homing endonuclease specificity through computational design and directed evolution

(2013) Summer B. Thyme et al.   NUCLEIC ACIDS RESEARCH

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

(2013) Sergey Lyskov et al.   PLoS One

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Fast Docking on Graphics Processing Units via Ray-Casting

(2013) Karen R. Khar et al.   PLoS One

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz

(2013) Rhiju Das   PLoS One

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Automating human intuition for protein design

(2013) Lucas G. Nivón et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

(2013) Hiromasa Yagi et al.   STRUCTURE

Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface

(2013) David K. Johnson et al.   PLoS Computational Biology

Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design

(2012) Summer B. Thyme et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

(2012) Christophe Schmitz et al.   JOURNAL OF MOLECULAR BIOLOGY

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

(2012) Fang-Chieh Chou et al.   NATURE METHODS

Accurate protein structure modeling using sparse NMR data and homologous structure information

(2012) J. M. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

(2012) O. F. Lange 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

Analysis and Modeling of the Variable Region of Camelid Single-Domain Antibodies

(2011) A. Sircar et al.   JOURNAL OF IMMUNOLOGY

Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings

(2011) Nikolaos G. Sgourakis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers

(2011) Chen Yanover et al.   NUCLEIC ACIDS RESEARCH

Modeling Symmetric Macromolecular Structures in Rosetta3

(2011) Frank DiMaio et al.   PLoS One

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

A Generic Program for Multistate Protein Design

(2011) Andrew Leaver-Fay et al.   PLoS One

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Real-Time PyMOL Visualization for Rosetta and PyRosetta

(2011) Evan H. Baugh et al.   PLoS One

Algorithm discovery by protein folding game players

(2011) F. Khatib et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

(2011) P. Sripakdeevong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation

(2011) Oliver F. Lange et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

A New Clustering of Antibody CDR Loop Conformations

(2010) Benjamin North et al.   JOURNAL OF MOLECULAR BIOLOGY

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting protein structures with a multiplayer online game

(2010) Seth Cooper et al.   NATURE

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

(2010) Justin Ashworth et al.   NUCLEIC ACIDS RESEARCH

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

NMR Structure Determination for Larger Proteins Using Backbone-Only Data

(2010) S. Raman et al.   SCIENCE

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

(2010) Aroop Sircar et al.   PLoS Computational Biology

Backbone flexibility in computational protein design

(2009) Daniel J Mandell et al.   CURRENT OPINION IN BIOTECHNOLOGY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Exploitation of binding energy for catalysis and design

(2009) Summer B. Thyme et al.   NATURE

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

(2009) Daniel J Mandell et al.   NATURE METHODS

Assessment of the optimization of affinity and specificity at protein–DNA interfaces

(2009) Justin Ashworth et al.   NUCLEIC ACIDS RESEARCH

RosettaAntibody: antibody variable region homology modeling server

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

Improved Energy Selection of Nativelike Protein Loops from Loop Decoys

(2008) Matthew S. Lin et al.   Journal of Chemical Theory and Computation

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability

(2008) Gregory D. Friedland et al.   JOURNAL OF MOLECULAR BIOLOGY

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

Toward high-resolution homology modeling of antibody Fvregions and application to antibody-antigen docking

(2008) Arvind Sivasubramanian et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS