Protein-Protein Docking with Dynamic Residue Protonation States

Computational design of a pH-sensitive IgG binding protein

(2014) E.-M. Strauch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Considering Protonation as a Posttranslational Modification Regulating Protein Structure and Function

(2013) André Schönichen et al.   Annual Review of Biophysics

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

Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock

(2013) Zhe Zhang et al.   PLoS One

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

The targets of CAPRI rounds 20-27

(2013) Joël Janin   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pH-selective mutagenesis of protein-protein interfaces:In silicodesign of therapeutic antibodies with prolonged half-life

(2013) Velin Z. Spassov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

(2013) Krishna Praneeth Kilambi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protonation and pK changes in protein–ligand binding

(2013) Alexey V. Onufriev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

(2013) Anne Lopes et al.   PLoS Computational Biology

Rapid Calculation of Protein pKa Values Using Rosetta

(2012) Krishna Praneeth Kilambi et al.   BIOPHYSICAL JOURNAL

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

Protein–protein binding affinity prediction on a diverse set of structures

(2011) Iain H. Moal et al.   BIOINFORMATICS

Towards the prediction of protein interaction partners using physical docking

(2011) M. N. Wass et al.   Molecular Systems Biology

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

(2011) Sidhartha Chaudhury et al.   PLoS One

Large shifts in pKa values of lysine residues buried inside a protein

(2011) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties

(2011) Arieh Warshel et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

(2011) Jens E. Nielsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformational Consequences of Ionization of Lys, Asp, and Glu Buried at Position 66 in Staphylococcal Nuclease

(2010) Daniel A. Karp et al.   BIOCHEMISTRY

Practically Useful: What the RosettaProtein Modeling Suite Can Do for You

(2010) Kristian W. Kaufmann et al.   BIOCHEMISTRY

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

(2010) S. Chaudhury et al.   BIOINFORMATICS

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

The HADDOCK web server for data-driven biomolecular docking

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

In silico modeling of pH-optimum of protein-protein binding

(2010) Rooplekha C. Mitra et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimating binding affinities by docking/scoring methods using variable protonation states

(2010) Min-Sun Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA

(2009) Annick Pollet et al.   FEBS Journal

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

(2009) Tim ten Brink et al.   Journal of Chemical Information and Modeling

The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening

(2009) Tuomo Kalliokoski et al.   Journal of Chemical Information and Modeling

Sensors and regulators of intracellular pH

(2009) Joseph R. Casey et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular determinants of the pKavalues of Asp and Glu residues in staphylococcal nuclease

(2009) Carlos A. Castañeda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

(2008) Sidhartha Chaudhury et al.   JOURNAL OF MOLECULAR BIOLOGY

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of pKa and redox properties in the thioredoxin superfamily

(2004) Efrosini Moutevelis et al.   PROTEIN SCIENCE