D. van der Spoel

Molecular Biology · 2000–2016

A researcher in the Science corpus: 16 papers; trusts 14 researchers and is trusted by 22 researchers here, as inferred from the citation graph.

Subfields

Molecular Biology — 66 citations into it; #3,658 of 17,773 by trust here, #1,710 by citations
Atomic and Molecular Physics, and Optics — 40 citations into it; #1,383 of 7,135 by trust here, #756 by citations
Materials Chemistry — 31 citations into it; #4,372 of 11,513 by trust here, #2,626 by citations
Computational Chemistry & Drug Discovery — 8 citations into it
Computational Theory and Mathematics — 8 citations into it; #6,933 of 12,182 by trust here, #1,936 by citations
Computational Biology & Bioinformatics — 7 citations into it
Spectroscopy — 7 citations into it; #313 of 1,674 by trust here, #131 by citations

Whom D. van der Spoel trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

Who trusts D. van der Spoel overall

Papers from D. van der Spoel's perspective

Ordered by how strongly the researchers D. van der Spoel trusts endorse each paper. Same corpus, a different order for every researcher.

A semiempirical free energy force field with charge‐based desolvation (Journal of Computational Chemistry)
Efficient docking of peptides to proteins without prior knowledge of the binding site (Protein Science)
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
CHARMM: The biomolecular simulation program
Numerical recipes in C
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters (International Conference on Software Composition)
Molecular modelling: Principles and applications
How Fast-Folding Proteins Fold (Science)
Everything you wanted to know about Markov State Models but were afraid to ask (Methods)
g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Their papers

GROMACS: Fast, flexible, and free (2005) — 17,374 citations
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (2008) — 15,253 citations
Efficient docking of peptides to proteins without prior knowledge of the binding site (2002) — 455 citations
g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates (2010) — 1,539 citations
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit (2013) — 7,077 citations
Potential for biomolecular imaging with femtosecond X-ray pulses (2000) — 1,811 citations
Water Determines the Structure and Dynamics of Proteins. (2016) — 817 citations
A temperature predictor for parallel tempering simulations. (2008) — 477 citations
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant (2011) — 687 citations
Toward prediction of functional protein pockets using blind docking and pocket search algorithms (2011) — 78 citations
The Origin of Layer Structure Artifacts in Simulations of Liquid Water. (2006) — 142 citations
Femtosecond diffractive imaging with a soft-X-ray free-electron laser (2006) — 966 citations
Linac Coherent Light Source (LCLS) Conceptual Design Report (2002) — 220 citations
Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials (2001) — 148 citations
GROMACS 3.0: a package for molecular simulation and trajectory analysis (2001) — 6,280 citations
Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation (2000) — 237 citations