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— CH. 1 · INTRODUCTION —

Dock

6 min listen · Ch. 1 of 6
6 sections
  • Dock is a word that means almost the opposite thing depending on which country uses it. The earliest known examples of it were found at Wadi al-Jarf, an ancient Egyptian harbor built for Pharaoh Khufu, dating from around 2500 BC on the Red Sea coast, where archaeologists also found anchors and storage jars nearby. Thousands of years before container ports and cruise terminals, people had already solved the same basic problem: how to bring a boat to land, load it, unload it, and send it out again safely. In American English, dock refers to the human-made structures themselves, usually on or near a shore. In British English, it means something else entirely: the water next to or around a wharf or quay. How the same word split into two meanings, and how engineers learned to control tides and currents to make it work, is where the story of the dock begins.

  • American English and British English took the word dock in different directions. In American usage, dock refers to one or a group of human-made structures involved in the handling of boats or ships, usually on or near a shore. In British usage, the same word instead means the area of water that is next to or around a wharf or quay, not the structure at all. The exact meaning still varies among different variants of the English language today. Dock can also refer to a dockyard, also known as a shipyard, where the loading, unloading, building, or repairing of ships occurs. A dockyard, in turn, consists of one or more docks, usually alongside other structures built to support them.

  • Wadi al-Jarf sits on the Red Sea coast, and its docks are the earliest known in the world, built for Pharaoh Khufu around 2500 BC. Archaeologists working the site also uncovered anchors and storage jars near the harbor structures, evidence of a working port rather than a ceremonial site. Nothing else discovered so far predates it. The find pushes the origin of dock building back to the very beginning of large-scale Egyptian seafaring, long before the word itself existed in any language spoken today.

  • At Lothal in India, a dock dating from 2400 BC was built deliberately away from the main current of the Sabarmati river, so silt would not build up and clog it. Modern oceanographers have concluded that the Harappans who built it must have understood tidal behavior in detail to place a dock on a river course that kept shifting. It stands as the earliest known dock in the world equipped to actually berth and service ships, rather than simply shelter them. Researchers believe Lothal's engineers studied tidal movements and how they affected brick construction, since the dock's walls were built from kiln-burnt brick able to withstand the water. That same tidal knowledge likely shaped where Lothal was founded in the first place. The nearby Gulf of Khambhat has the highest tidal amplitude in the region, letting ships be sluiced through the river estuary on incoming flow tides. The structure the engineers built was trapezoidal, with north-south arms averaging 21.8 metres and east-west arms of 37 metres.

  • In British usage, a dock is an enclosed area of water for loading, unloading, building, or repairing ships, made either by building harbour walls into an existing body of water or by excavating dry land. Among the specific types, a wet dock, also called an impounded dock, holds water in place using dock gates or a lock, keeping ships afloat at low tide even where the tidal range is large. It functions like a lock, controlling water level while still allowing ships to pass in and out, which makes transferring cargo far easier. The world's first enclosed wet dock with lock gates was the Howland Great Dock on the River Thames, built in 1703, though it amounted to little more than a haven surrounded by trees with no facilities for unloading. The world's first commercial enclosed wet dock, complete with quays and unloading warehouses, was the Old Dock at Liverpool, built in 1715 and able to hold up to 100 ships at once. It cut ship waiting times and sped up turnarounds, sharply improving how much cargo could move through. A drydock works differently: it also uses dock gates, but can be emptied of water entirely so the underwater parts of a ship can be inspected and repaired. A floating dry dock takes that idea further, using a submersible structure to lift ships clear of the water in places with no land-based dock facilities at all. Where water level is not controlled, berths are described as floating, meaning there is always enough water to keep a ship afloat, or as NAABSA, an acronym for Not Always Afloat But Safely Aground, where ships settle on the bottom at low tide and must be built to withstand it.

  • In American English, dock is technically synonymous with pier or wharf, covering any human-made structure in the water meant for people to stand on. In practice, though, pier tends to describe structures originally built for industrial use, such as seafood processing or shipping, and more recently for cruise ships, while dock covers almost everything else, often paired with a qualifier like ferry dock, swimming dock, or ore dock. Pier also commonly describes wooden or metal structures that extend into the ocean from beaches, built mainly to let people fish without needing a boat. The water area between piers has its own name in American English: a slip. Away from major ports, in the cottage country shared by parts of the United States and Canada, a dock is simply a wooden platform built over water, one end secured to the shore, used for boarding and offloading small boats. From a monumental ancient harbor tuned to the tides of the Gulf of Khambhat to a plank platform at the edge of a lake, the same word still describes the same basic act of meeting the water halfway.

Common questions

Who created the DOCK molecular docking program?

DOCK was created in the 1980s by Irwin "Tack" Kuntz's group at UCSF. It is the first docking program ever developed. Codevelopers include Brian K. Shoichet, David A. Case, and Robert C. Rizzo.

What algorithms does DOCK use to predict molecular binding?

DOCK uses geometric algorithms, including a shape-matching method that places spheres in a protein's binding pocket and performs bipartite matching between those spheres and a candidate molecule. This rigid docking approach is present in all versions of the program.

How does DOCK handle flexible ligands?

DOCK accounts for ligand flexibility using two methods: an algorithm called anchor and grow (versions 4-6), and hierarchical docking of databases (versions 3.5-3.7). Anchor and grow works by fixing a rigid substructure of the molecule in the pocket, then building out flexible portions incrementally.

What is AMBER score in DOCK 6?

AMBER score is a scoring function implemented into DOCK version 6 by David A. Case's group via a molecular dynamics engine. It accounts for receptor flexibility and ranks compounds by their binding energy across energetic ensembles rather than a single static pose.

What versions of DOCK are currently being developed?

Two versions are actively developed: DOCK 6 and DOCK 3. They represent distinct lines of the original program suited to different needs in computational chemistry and drug discovery.

What is DOCK used for in drug discovery?

DOCK predicts the binding modes of small molecules to protein targets, a process central to structure-based drug discovery. Its methods support both rigid and flexible ligand docking as well as large-scale virtual screening of compound databases.

All sources

6 references cited across the entry

  1. 5BookLothal re-visitation Project, a fine thread connecting Intis to contemporary Raveena (Via Oman)D. Frenez — BAR — 2014
  2. 6NYPE 2015 Time Charter Party, explanatory notesBaltic and International Maritime Council et al.