Martin Zacharias
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Computer Science
Martin Zacharias's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science University of California, Berkeley
- Bachelors Computer Science University of California, Berkeley
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(Suggest an Edit or Addition)Martin Zacharias's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration (1994) (423)
- Protein–protein docking with a reduced protein model accounting for side‐chain flexibility (2003) (322)
- A family of macrodomain proteins reverses cellular mono-ADP-ribosylation (2013) (282)
- NWChem: Past, present, and future. (2020) (269)
- A molecular mechanics/grid method for evaluation of ligand–receptor interactions (1995) (162)
- Single-molecule dissection of stacking forces in DNA (2016) (152)
- Accounting for conformational changes during protein-protein docking. (2010) (152)
- A statistical analysis of random mutagenesis methods used for directed protein evolution. (2006) (147)
- Community-wide assessment of protein-interface modeling suggests improvements to design methodology. (2011) (139)
- Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach (2011) (138)
- EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results (2010) (136)
- The interface of protein-protein complexes: Analysis of contacts and prediction of interactions (2008) (131)
- Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking (2008) (120)
- Conformational Flexibility of the MHC Class I α1-α2 Domain in Peptide Bound and Free States: A Molecular Dynamics Simulation Study (2004) (119)
- Effective Dephosphorylation of Src Substrates by SHP-1* (2004) (110)
- Dissecting protein–RNA recognition sites (2008) (109)
- ATTRACT: Protein–protein docking in CAPRI using a reduced protein model (2005) (106)
- Accounting for global protein deformability during protein-protein and protein-ligand docking. (2005) (104)
- Multi-domain structure and correlated dynamics determined by self-consistent FRET networks (2016) (103)
- Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing‐potential (2006) (100)
- Prediction of antigenic epitopes on protein surfaces by consensus scoring (2009) (100)
- Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions (2013) (96)
- Fully Blind Peptide-Protein Docking with pepATTRACT. (2015) (94)
- CHARMM-GUI supports the Amber force fields. (2020) (94)
- Accounting for loop flexibility during protein–protein docking (2005) (94)
- Tapasin and other chaperones: models of the MHC class I loading complex (2004) (93)
- Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis (2019) (93)
- Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP (2004) (87)
- Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. (2008) (84)
- In silico prediction of binding sites on proteins. (2010) (83)
- A web interface for easy flexible protein-protein docking with ATTRACT. (2015) (81)
- Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation. (2007) (79)
- Effect of the F610A mutation on substrate extrusion in the AcrB transporter: explanation and rationale by molecular dynamics simulations. (2011) (78)
- Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2‐ and tac promoter on growth‐rate control and stringent sensitivity. (1989) (77)
- The Architecture of Talin1 Reveals an Autoinhibition Mechanism (2019) (77)
- Local and global effects of strong DNA bending induced during molecular dynamics simulations (2009) (72)
- Computational prediction of protein–protein binding affinities (2019) (71)
- Comparative molecular dynamics analysis of tapasin‐dependent and ‐independent MHC class I alleles (2006) (71)
- Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus (2013) (70)
- The pepATTRACT web server for blind, large-scale peptide–protein docking (2017) (69)
- Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility (2011) (69)
- Binding site prediction and improved scoring during flexible protein–protein docking with ATTRACT (2010) (69)
- PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces (2014) (68)
- Prediction of protein-protein interaction sites using electrostatic desolvation profiles. (2010) (67)
- Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. (2016) (66)
- Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study (2005) (66)
- Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain. (2006) (65)
- Sequence Specificity of SHP-1 and SHP-2 Src Homology 2 Domains (2006) (63)
- Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: a molecular dynamics simulation study. (2009) (62)
- Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins. (2013) (62)
- Poisson-Boltzmann analysis of the lambda repressor-operator interaction. (1992) (60)
- Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: a molecular dynamics simulation study. (2008) (59)
- Hereditary lattice corneal dystrophy is associated with corneal amyloid deposits enclosing C-terminal fragments of keratoepithelin. (2005) (59)
- Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study. (2004) (57)
- Analysis of the Fis-dependent and Fis-independent transcription activation mechanisms of the Escherichia coli ribosomal RNA P1 promoter. (1992) (57)
- Dipeptides promote folding and peptide binding of MHC class I molecules (2013) (56)
- Sensitive Assay for Laboratory Evolution of Hydroxylases toward Aromatic and Heterocyclic Compounds (2005) (55)
- Blind prediction of interfacial water positions in CAPRI (2014) (55)
- Folding simulations of Trp‐cage mini protein in explicit solvent using biasing potential replica‐exchange molecular dynamics simulations (2009) (54)
- RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. (2006) (54)
- Subnanometre enzyme mechanics probed by single-molecule force spectroscopy (2016) (53)
- A coarse-grained force field for Protein–RNA docking (2011) (53)
- B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations. (2006) (52)
- Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells (2019) (52)
- iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement (2015) (52)
- ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps (2012) (52)
- Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility (2007) (52)
- DAPI binding to the DNA minor groove: a continuum solvent analysis (2002) (51)
- Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations (1992) (50)
- Cytokine-induced Paracrystals Prolong the Activity of Signal Transducers and Activators of Transcription (STAT) and Provide a Model for the Regulation of Protein Solubility by Small Ubiquitin-like Modifier (SUMO)* (2011) (49)
- Enzymatic Degradation of β‐ and Mixed α,β‐Oligopeptides (2006) (49)
- Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex (1999) (48)
- Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations. (2007) (48)
- Free energy analysis and mechanism of base pair stacking in nicked DNA (2016) (46)
- Flexible docking and refinement with a coarse‐grained protein model using ATTRACT (2013) (43)
- Peptide binding to MHC class I and II proteins: new avenues from new methods. (2010) (43)
- Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. (1994) (42)
- SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. (2016) (41)
- Exploiting Antigenic Diversity for Vaccine Design (2010) (41)
- Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly (2017) (40)
- Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis (2015) (40)
- Atomic resolution model of the antibody Fc interaction with the complement C1q component. (2012) (40)
- PTools: an opensource molecular docking library (2009) (40)
- Continuum Solvent Modeling of Nonpolar Solvation: Improvement by Separating Surface Area Dependent Cavity and Dispersion Contributions (2003) (40)
- Maturation of the 5S rRNA 5' end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii. (2008) (39)
- Tackling the challenges posed by target flexibility in drug design (2010) (39)
- Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model. (1999) (39)
- Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations. (2009) (39)
- Minor groove deformability of DNA: a molecular dynamics free energy simulation study. (2006) (38)
- Transformations in plasma membranes of cancerous cells and resulting consequences for cation insertion studied with molecular dynamics. (2013) (38)
- Evaluation of Predicted Protein-Protein Complexes by Binding Free Energy Simulations. (2019) (37)
- Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study. (2006) (36)
- Protein-DNA docking with a coarse-grained force field (2012) (36)
- Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach. (2009) (36)
- Harmonic modes as variables to approximately account for receptor flexibility in ligand–receptor docking simulations: Application to DNA minor groove ligand complex (1999) (35)
- Crystal structures of the free and ligand-bound FK1-FK2 domain segment of FKBP52 reveal a flexible inter-domain hinge. (2013) (35)
- Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments (2010) (35)
- Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials (2014) (34)
- Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli. (1991) (34)
- The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study (2015) (33)
- Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. (2006) (33)
- Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators (2019) (33)
- Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study. (2006) (32)
- Elastic Network Models of Nucleic Acids Flexibility. (2013) (32)
- Bovine Serum Albumin and Lysozyme Adsorption on Calcium Phosphate Particles (2010) (31)
- Efficient inclusion of receptor flexibility in grid‐based protein–ligand docking* (2011) (31)
- Molecular determinants for high-affinity block of human EAG potassium channels by antiarrhythmic agents. (2004) (30)
- The structure and oxidation of the eye lens chaperone αA-crystallin (2019) (30)
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices (2018) (30)
- The temperature dependence of the helical twist of DNA (2018) (29)
- From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations. (2017) (29)
- Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites (2008) (29)
- Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules. (2009) (28)
- Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method. (2009) (28)
- Fatal amyloid formation in a patient’s antibody light chain is caused by a single point mutation (2020) (28)
- Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations. (2009) (28)
- Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange. (2008) (28)
- RAID3 - An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity (2015) (27)
- A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine (2019) (27)
- Designed Macrocyclic Peptides as Nanomolar Amyloid Inhibitors Based on Minimal Recognition Elements. (2018) (27)
- Inversion of receptor binding preferences by mutagenesis: free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins. (1993) (26)
- Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations. (2001) (26)
- Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles (2014) (25)
- Stoichiometry of HLA Class II-Invariant Chain Oligomers (2011) (25)
- γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding (2019) (25)
- Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection (2020) (25)
- Exploring biomolecular dynamics and interactions using advanced sampling methods (2015) (25)
- Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation. (2014) (25)
- The importance of individual nucleotides for the structure and function of rRNA molecules in E. coli (1986) (24)
- Structural and dynamic properties of cytochrome P450 BM‐3 in pure water and in a dimethylsulfoxide/water mixture (2005) (24)
- Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations (2014) (24)
- How to Efficiently Include Receptor Flexibility During Computational Docking (2008) (23)
- Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions. (1997) (23)
- Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling (2013) (22)
- Protein‐protein and peptide‐protein docking and refinement using ATTRACT in CAPRI (2017) (22)
- Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta (2015) (22)
- A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA (2005) (22)
- Proline substitution independently enhances H‐2Db complex stabilization and TCR recognition of melanoma‐associated peptides (2013) (22)
- Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations. (2009) (22)
- Multiscale Simulation of Receptor-Drug Association Kinetics: Application to Neuraminidase Inhibitors. (2017) (21)
- A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions. (2016) (21)
- Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. (2005) (21)
- Prediction of protein–protein complexes using replica exchange with repulsive scaling (2020) (21)
- Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations. (2015) (21)
- Structural Modeling of γ-Secretase Aβ n Complex Formation and Substrate Processing. (2019) (21)
- The signal for growth rate control and stringent sensitivity in E. coli is not restricted to a particular sequence motif within the promoter region. (1990) (20)
- The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation. (2015) (20)
- Structure and target interaction of a G-quadruplex RNA-aptamer (2016) (20)
- Influence of 8-oxoguanosine on the fine structure of DNA studied with biasing-potential replica exchange simulations. (2013) (20)
- Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations. (2014) (20)
- Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations. (2014) (20)
- Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail (2017) (20)
- ATTRACT and PTools: open source programs for protein-protein docking. (2012) (19)
- Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations. (2004) (19)
- Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent (2011) (19)
- Determinants of the assembly and function of antibody variable domains (2017) (19)
- TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism (2008) (19)
- Temperature dependence of looping rates in a short peptide. (2007) (19)
- gp130 activation is regulated by D2-D3 interdomain connectivity. (2013) (19)
- Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins (2016) (19)
- How methyl–sugar interactions determine DNA structure and flexibility (2018) (19)
- Effect of 8-oxoguanine on DNA structure and deformability. (2013) (19)
- Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations (2009) (18)
- Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies. (2010) (18)
- Conformational deformability of RNA: a harmonic mode analysis. (2000) (18)
- Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation. (2001) (17)
- A Novel Family of Human Leukocyte Antigen Class II Receptors May Have Its Origin in Archaic Human Species* (2013) (17)
- Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach (2016) (17)
- Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations. (2017) (17)
- Mapping the spatial neighborhood of the regulatory 6S RNA bound to Escherichia coli RNA polymerase holoenzyme. (2013) (17)
- Uncovering the Binding Mode of γ -Secretase Inhibitors. (2019) (16)
- A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains* (2014) (16)
- Accurate modeling of DNA conformational flexibility by a multivariate Ising model (2021) (16)
- Efficient calculation of relative binding free energies by umbrella sampling perturbation (2014) (16)
- Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis (2016) (16)
- Molecular mechanism of amyloidogenic mutations in hypervariable regions of antibody light chains (2021) (16)
- Covalent dye attachment influences the dynamics and conformational properties of flexible peptides (2017) (16)
- Functional characterization of a putative internal promoter sequence between the 16S and the 23S RNA genes within the Escherichia coli rrnB operon (1989) (15)
- Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent (2010) (15)
- New insights into the role of the glutamic acid of the E‐box motif in group B Streptococcus pilus 2a assembly (2012) (15)
- Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping (2009) (15)
- Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis. (2003) (14)
- Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. (2020) (14)
- Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase. (2015) (14)
- Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations. (2017) (14)
- Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations (2011) (14)
- Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling. (2016) (14)
- Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage (2017) (13)
- Tumuc1: A New Accurate DNA Force Field Consistent with High-Level Quantum Chemistry. (2021) (13)
- An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA (2015) (13)
- Monte Carlo replica‐exchange based ensemble docking of protein conformations (2017) (13)
- Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations. (2014) (13)
- Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides. (2004) (13)
- Mechanism of Reversible Peptide-Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study. (2016) (13)
- Structural and Dynamic Properties of the CAGQW Peptide in Water: A Molecular Dynamics Simulation Study Using Different Force Fields (2004) (13)
- Polyacrylamide gradient gel electrophoresis for the detection of bended DNA fragments. (1990) (12)
- ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease (2012) (12)
- Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential (2017) (12)
- Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins. (2012) (12)
- Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA (2016) (12)
- Modeling large protein–glycosaminoglycan complexes using a fragment‐based approach (2019) (12)
- The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions (1990) (11)
- Role of tyrosine hot‐spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study (2013) (11)
- Protein-Protein Complexes: Analysis, Modeling and Drug Design (2010) (11)
- Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state (2010) (11)
- RNA aptamers as potential pharmaceuticals against infections with African trypanosomes. (2006) (11)
- The dynamics of γ-secretase and its substrates. (2020) (11)
- DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study (2012) (10)
- Scoring optimisation of unbound protein–protein docking including protein binding site predictions (2012) (10)
- Update of the ATTRACT force field for the prediction of protein–protein binding affinity (2017) (10)
- Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD (2021) (10)
- Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. (2019) (10)
- Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling (2020) (10)
- Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling. (2018) (10)
- Rapid in silico Design of Potential Cyclic Peptide Binders Targeting Protein-Protein Interfaces (2020) (10)
- Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation. (2017) (9)
- Theoretical studies of nucleic acids folding (2014) (9)
- Design and biological evaluation of linear and cyclic phosphopeptide ligands of the N-terminal SH2 domain of protein tyrosine phosphatase SHP-1. (2005) (9)
- Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations (2014) (9)
- The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding. (2019) (9)
- Redirecting catalysis from proteolysis to perhydrolysis in subtilisin Carlsberg. (2013) (9)
- Reengineering of subtilisin Carlsberg for oxidative resistance (2013) (8)
- Comparative Molecular Dynamics Analysis of RNase-S Complex Formation. (2017) (8)
- Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation (2020) (8)
- Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding (2022) (8)
- Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2 (2002) (8)
- Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations. (2016) (8)
- Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series (2020) (8)
- Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation. (2020) (8)
- An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27. (2019) (8)
- Deletions in the tL structure upstream to the rRNA genes in the E. coli rrnB operon cause transcription polarity. (1987) (8)
- Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations (2017) (8)
- Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking (2017) (7)
- Altered Hinge Conformations in APP Transmembrane Helix Mutants May Affect Enzyme-Substrate Interactions of γ-Secretase. (2020) (7)
- Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach (2019) (7)
- From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation (2020) (7)
- How Mutations perturb γ-Secretase active site studied by Free Energy Simulations. (2020) (7)
- Free energy calculations elucidate substrate binding, gating mechanism, and tolerance‐promoting mutations in herbicide target 4‐hydroxyphenylpyruvate dioxygenase (2019) (7)
- Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins. (2016) (7)
- Results of interspecific and intergeneric crosses in the Gramineae in relation to natural reproductive isolating mechanisms. (1980) (7)
- Modeling Protein–Glycosaminoglycan Complexes: Does the Size Matter? (2021) (7)
- Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans (2021) (6)
- A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain. (2015) (6)
- How global DNA unwinding causes non-uniform stress distribution and melting of DNA (2020) (6)
- Molecular mechanism of Be2+-ion binding to HLA-DP2: tetrahedral coordination, conformational changes and multi-ion binding. (2019) (6)
- Influence of a cis,syn‐cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations (2015) (6)
- Phosphorylation of Ser111 in Rab8a modulates Rabin8 dependent activation by perturbation of side chain interaction networks. (2019) (6)
- Phosphorylation of Ser111 in Rab8a modulates Rabin8 dependent activation by perturbation of side chain interaction networks (2019) (6)
- Regulation of Ribosomal RNA Synthesis and Control of Ribosome Formation in E. Coli (1993) (6)
- Rapid alchemical free energy calculation employing a generalized born implicit solvent model. (2015) (5)
- Path Dependence of Free Energy Components in Thermodynamic Integration (1995) (5)
- Thermodynamics and Kinetics of Nucleobase Stacking Oligomerization Revealed by Molecular Dynamics Simulations. (2017) (5)
- The human T-cell lymphotropic virus type-I dimerization initiation site forms a hairpin loop, unlike previously characterized retroviral dimerization motifs. (2004) (5)
- Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts (2021) (4)
- Syntheses and activities of backbone‐side chain cyclic octapeptide ligands with N‐functionalized phosphotyrosine for the N‐terminal SH2‐domain of the protein tyrosine phosphatase SHP‐1 (2010) (4)
- Phosphopeptide Ligands of the SHP‐1 N‐SH2 Domain: Effects on Binding and Stimulation of Phosphatase Activity (2006) (4)
- A single residue switch reveals principles of antibody domain integrity (2018) (4)
- Effect O6‐guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations (2015) (4)
- Mechanistic principles of an ultra-long bovine CDR reveal strategies for antibody design (2021) (4)
- Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules (2016) (4)
- Structural dynamics in the evolution of a bilobed protein scaffold (2021) (4)
- Dissociation of β2m from MHC Class I Triggers Formation of Noncovalent, Transient Heavy Chain Dimers (2021) (4)
- Designed Macrocyclic Peptides as Nanomolar Amyloid Inhibitors Based on Minimal Recognition Elements (2018) (4)
- Cytokine-induced paracrystals prolong the activity of signal transducers and activators of transcription (STAT) and provide a model for the regulation of protein solubility by small ubiquitin-like modifier (SUMO). (2017) (4)
- Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands (2006) (3)
- 9. Scoring and Refinement of Predicted Protein–Protein Complexes (2010) (3)
- Uncovering the Binding Mode of γ-Secretase Inhibitors (2019) (3)
- Efficient Search on Energy Minima for Structure Prediction of Nucleic Acid Motifs (2004) (3)
- Benchmarking biomolecular force field‐based Zn2+ for mono‐ and bimetallic ligand binding sites (2022) (3)
- Computer Modelling and Molecular Dynamics Simulation of Biomolecules (2019) (3)
- Fast and accurate grid representations for atom‐based docking with partner flexibility (2017) (3)
- Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling (2021) (3)
- ADAMTS4-specific MR probe to assess aortic aneurysms in vivo using synthetic peptide libraries (2022) (3)
- Mechanism of collagen folding propagation studied by Molecular Dynamics simulations (2021) (3)
- Reduced Protein Model as a Tool in the Homology Modeling (2003) (2)
- Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations. (2021) (2)
- Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations (2020) (2)
- Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surfaces. (2014) (2)
- Targeting telomeres: Molecular dynamics and free energy simulation of gold-carbene binding to DNA. (2020) (2)
- Explicit solvent repulsive scaling replica exchange molecular dynamics (RS‐REMD) in molecular modeling of protein‐glycosaminoglycan complexes (2022) (2)
- Global Dynamics of Yeast Hsp90 Middle and C-Terminal Dimer Studied by Advanced Sampling Simulations (2019) (2)
- Examining the potency of suggested inhibitors for the phosphatase activity of the human soluble epoxide hydrolase by molecular dynamics simulations (2010) (2)
- Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS. (2021) (2)
- Characterization of Transiently Stable Structural Motifs in Intrinsically Disordered Proteins using Free Energy Simulations (2015) (2)
- Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series. (2021) (2)
- Fragment-based modeling of protein-bound ssRNA (2016) (1)
- An internal docking site stabilizes substrate binding to γ-secretase: Analysis by Molecular Dynamics Simulations. (2022) (1)
- Protein-protein docking refinement using restraint molecular dynamics simulations (2016) (1)
- Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function (2021) (1)
- Intramembrane client recognition potentiates the chaperone functions of calnexin (2022) (1)
- Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations (2022) (1)
- Protein-DNA docking with a coarse-grained force field (2012) (1)
- 163 Enhanced sampling of peptides and proteins with a new biasing replica exchange method (2013) (1)
- A constant domain mutation in a patient-derived antibody light chain reveals principles of AL amyloidosis (2023) (1)
- Evolution of structural dynamics in bilobed proteins (2020) (1)
- Determination of structural ensembles and correlated dynamics of a multi-domain protein (2017) (1)
- Molecular architectures of the 24meric eye lens chaperone alphaB- crystallin elucidated by a triple hybrid approach (2011) (1)
- Correction for Schickinger et al., Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices (2018) (1)
- Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs Within 100 ns. (2020) (1)
- Free Energy Calculations of Ligand–Protein Binding (2015) (1)
- Modulation of SHP-1 phosphatase activity by monovalent and bivalent SH2 phosphopeptide ligands. (2010) (1)
- Poisson-Boltzmann analysis of the X repressor-operator interaction (2005) (1)
- Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS (2020) (1)
- The human signal peptidase complex acts as a quality control enzyme for membrane proteins (2022) (1)
- Dynamics of the full-length yeast Hsp90 dimer (2019) (1)
- The importance of individual nucleotides for the structure and function of rRNA molecules in E. coli: A mutagenesis study (1986) (2002) (1)
- Computational Tools for Accurate Binding Free-Energy Prediction. (2021) (1)
- Predicting Allosteric Changes from Conformational Ensembles. (2017) (1)
- Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids (2012) (1)
- Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations (2019) (1)
- Chapter 9:Accounting for Target Flexibility During Ligand–Receptor Docking (2012) (1)
- Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications. (2022) (1)
- Synthetic strategies to a backbone-side chain cyclic SHP-1 N-SH2 ligand containing N-functionalized alkyl phosphotyrosine. (2010) (0)
- Structure Resource Fully Blind Peptide-Protein Docking with pepATTRACT (2015) (0)
- Faculty Opinions recommendation of Adhesive water networks facilitate binding of protein interfaces. (2011) (0)
- Fast peptide exchange on major histocompatibility complex class I molecules by acidic stabilization of a peptide‐empty intermediate (2022) (0)
- Issue Information (2021) (0)
- Amyloid fibril structure from the vascular variant of systemic AA amyloidosis (2022) (0)
- Mechanism of β‐hairpin formation in AzoChignolin and Chignolin (2022) (0)
- Activation of a D‐form of rabbit muscle glycogen synthase by Ca2+‐activated protease (1986) (2002) (0)
- Faculty Opinions recommendation of Structural control of crystal nuclei by an eggshell protein. (2010) (0)
- Mutant immunoglobulin light chain causing amyloidosis (Pat-1) (2020) (0)
- Peptide selection for binding to MHC class I : insights from structure and molecular dynamics (2013) (0)
- Cryo-EM structure of autoinhibited human talin-1 (2019) (0)
- Disordered Toxin: The Mechanism of Transcription Regulation of the Pseudomonas Putida GraTA Operon (2017) (0)
- Biomolecular Simulation of Base Excision Repair and Protein Signaling (2006) (0)
- Hamiltonian Replica Exchange Simulation (2013) (0)
- MECHANISM SECURING ‘γ-SECRETASE-APP/Aβ’ COMPLEXES AND REGULATING Aβ LENGTH (2019) (0)
- Flexible Protein-Protein Docking (2011) (0)
- The Prominence of the Ligand Peptide Carboxyl Terminus in the MHC Class I Molecules Stability and Affinity (2014) (0)
- QuaMo-Toolbox Tutorial (2002) (0)
- Dissociation of β2m from cell surface MHC class I triggers formation of noncovalent, transient heavy chain dimers (2021) (0)
- Conformational Transitions in Switch Regions of the Ras-Like GTPase Rab1B Studied by Free Energy Simulations (2015) (0)
- Water model determines thermosensitive and physicochemical properties of poly(N-isopropylacrylamide) in molecular simulations (2023) (0)
- Integrative Modeling of the ISWI Chromatin Remodeling Enzyme from Cross-Linking/Mass Spectrometry and Saxs Data (2016) (0)
- Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations. (2022) (0)
- Base pairing and stacking contributions to double stranded DNA formation (2020) (0)
- The development of nucleic acids force fields: From an unchallenged past to a competitive future. (2022) (0)
- Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock (2022) (0)
- Enzyme–substrate interface targeting by imidazole‐based γ‐secretase modulators activates γ‐secretase and stabilizes its interaction with APP (2022) (0)
- Determinants of the assembly and function of antibody variable domains (2017) (0)
- Refinement Of Protein Model Structures In Explicit Solvent Using Biasing Potential Replica Exchange Simulations (2009) (0)
- HP24wt derived from the villin headpiece subdomain (2015) (0)
- Rapid protein-ligand docking using soft modes from MD simulations to account for protein deformability: application to protein kinase-ligand interactions (2005) (0)
- Crystal structure of the human protein-proximal ADP-ribosyl-hydrolase MacroD2 (2013) (0)
- Allosteric Communication in Rnd1 and Rac1 Association with the Plexin-B1 RhoGTPase Binding Domain Revealed by Hydrogen Exchange Mass Spectroscopy and by Solution NMR (2015) (0)
- Prediction of protein–protein complex structures by docking (2020) (0)
- Author response: Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail (2016) (0)
- Front Cover: Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series (15/2021) (2021) (0)
- Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding (2022) (0)
- What Makes a Good Protein–Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism (2023) (0)
- Investigating Complex Formation of C99 with Gamma-Secretase, Using Atomistic MM-MD Simulations and Free Energy Calculations (2018) (0)
- Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection (2020) (0)
- The relationship between protein dynamics and function for the MHC class I antigen presenting molecule (2012) (0)
- Toward Force Fields with Improved Base Stacking Descriptions. (2023) (0)
- Backbone 1H, 15N, 13C chemical shift assignments for the MAK33 CH2 antibody domain (2018) (0)
- The structure and oxidation of the eye lens chaperone αA-crystallin (2019) (0)
- Conformational preferences of SH2 domains in free and ligand-bound states studied by molecular dynamics simulations (2001) (0)
- Global Deformation of DNA Facilitates Recognition and Nucleotide Flipping of Damaged Sites: A Molecular Dynamics Simulation Study (2016) (0)
- Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions. (2017) (0)
- Influence of a Ser111‐phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations (2021) (0)
- Crystal structure of H-2Kb with a disulfide stabilized F pocket in complex with the LCMV derived peptide GP34 (2014) (0)
- Crystal Structure Analysis of FKBP52, Crystal Form III (2013) (0)
- RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function (2005) (0)
- Fragment based modeling of protein-GAG complexes (2017) (0)
- A Knowledge-Based Potential for Protein-RNA Docking (2008) (0)
- Rapid peptide exchange on MHC class I by small molecules elucidates dynamics of bound peptide (2022) (0)
- Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis (2022) (0)
- Development and Application of a Fully Blind Flexible Peptide-protein Docking Protocol, pepATTRACT (2016) (0)
- Author response: Fatal amyloid formation in a patient’s antibody light chain is caused by a single point mutation (2020) (0)
- Dynamical Properties of Flexible Peptides are Modified by Covalent Fluorophore Attachment: A Combined Fluorescence and Molecular Dynamics Study (2017) (0)
- i-ATTRACT: a New Flexible Docking Approach for Investigating Protein Protein Interactions (2014) (0)
- Backbone 1H, 15N, 13C chemical shift assignments for MAK33 EV-CH2-SK antibody domain extended variant (2018) (0)
- Structural Dynamics of Hsp90 Resolved by a Novel Multi-Pair FRET Approach (2016) (0)
- Abstract B049: Empty MHC class I molecules for improved detection of antigen-specific T-cells (2019) (0)
- Dipeptides enhance folding and peptide binding of “empty” MHC class I molecules (P5002) (2013) (0)
- Influence of DNA Conformation and Repair Enzyme on Guanine and 8-Oxoguanine Base Flipping (2015) (0)
- Dynamics of the full-length yeast Hsp90 dimer (2019) (0)
- Pseudo-atomic model of a 16-mer assembly of reduced recombinant human alphaA-crystallin (non domain swapped configuration) (2019) (0)
- Crystal Structure Analysis of FKBP52, Complex with FK506 (2013) (0)
- Rapid Rational Design of Cyclic Peptides Mimicking Protein-Protein Interfaces. (2022) (0)
- Electrostatic profiles of targets NMB0033 and CT043 (2008) (0)
- Match_Motif: A rapid computational tool to assist in protein–protein interaction design (2021) (0)
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What Schools Are Affiliated With Martin Zacharias?
Martin Zacharias is affiliated with the following schools:
