Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop

Self-Assembly of an Aspartate-Rich Sequence from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations and Experiments

(2014) Phanourios Tamamis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Predictive Model for HIV Type 1 Coreceptor Selectivity

(2013) Chris A. Kieslich et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop

(2013) Phanourios Tamamis et al.   BIOPHYSICAL JOURNAL

Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures

(2013) Ronald D. Gorham et al.   EXPERIMENTAL EYE RESEARCH

Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An Implicit Membrane Model with a Dynamically Varying Bilayer Thickness

(2013) Afra Panahi et al.   Journal of Chemical Theory and Computation

Interplay between Drying and Stability of a TIM Barrel Protein: A Combined Simulation–Experimental Study

(2013) Payel Das et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Characterization of a dual-tropic Human immunodeficiency virus (HIV-1) strain derived from the prototypical X4 isolate HXBc2

(2013) Shi-hua Xiang et al.   VIROLOGY

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

(2013) Katarzyna Bozek et al.   PLoS Computational Biology

Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs

(2012) Phanourios Tamamis et al.   Chemical Biology & Drug Design

Importance of V3 Loop Flexibility and Net Charge in the Context of Co-Receptor Recognition. A Molecular Dynamics Study on HIV gp120

(2012) Chandramouli Balasubramanian et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Structural dynamics of V3 loop with different electrostatics: implications on co-receptor recognition: a molecular dynamics study of HIV gp120

(2012) Balasubramanian Chandramouli et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Membrane protein native state discrimination by implicit membrane models

(2012) Olga Yuzlenko et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

(2012) Meghan L. Bellows-Peterson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops

(2012) Aliana López de Victoria et al.   PLoS One

Allosteric Model of Maraviroc Binding to CC Chemokine Receptor 5 (CCR5)

(2011) Javier Garcia-Perez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Theoretical Studies on the Interactions and Interferences of HIV-1 Glycoprotein gp120 and Its Coreceptor CCR5

(2011) Lin-tai Da et al.   Journal of Chemical Information and Modeling

The Conformation and Orientation of a 27-Residue CCR5 Peptide in a Ternary Complex with HIV-1 gp120 and a CD4-Mimic Peptide

(2011) Einat Schnur et al.   JOURNAL OF MOLECULAR BIOLOGY

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin

(2011) Phanourios Tamamis et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MEDELLER: homology-based coordinate generation for membrane proteins

(2010) Sebastian Kelm et al.   BIOINFORMATICS

Discovery of Entry Inhibitors for HIV-1 via a New De Novo Protein Design Framework

(2010) M.L. Bellows et al.   BIOPHYSICAL JOURNAL

New Compstatin Variants through Two De Novo Protein Design Frameworks

(2010) M.L. Bellows et al.   BIOPHYSICAL JOURNAL

Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations

(2010) Phanourios Tamamis et al.   JOURNAL OF NON-CRYSTALLINE SOLIDS

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

(2010) Ambrish Roy et al.   Nature Protocols

Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists

(2010) B. Wu et al.   SCIENCE

CHARMM: The biomolecular simulation program

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

Amyloid-Like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations

(2009) Phanourios Tamamis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Two HIV-1 Variants Resistant to Small Molecule CCR5 Inhibitors Differ in How They Use CCR5 for Entry

(2009) Reem Berro et al.   PLoS Pathogens

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY